Acquisition - Department of Chemistrycic/nmr/Guides/Bruker_AVANCE...This manual is written for Avance spectrometers. Nevertheless, a large part of it is also valid for older spectrometers

Copyright (C) 2001 by Bruker BioSpin GmbHAll rights reserved. No part of this publication may be reproduced, stored in a retrieval sys-tem, or transmitted, in any form, or by any means without the prior consent of the publisher.

Part-No: H9775A3

10.04.2002

Acquisition

Reference Manual

DONE

INDEX

INDEX

Product names used are trademarks or registered trademarks of their respective holders.

Bruker software support is available via phone, fax, e-mail, Internet, or ISDN.Please contact your local office, or directly:

Address: Bruker BioSpin GmbHSoftware DepartmentSilberstreifenD-76287 RheinstettenGermany

Phone: +49 (721) 5161 440Fax: +49 (721) 5161 480E-mail: [email protected]: ftp.bruker.de / ftp.bruker.comWWW: www.bruker.de / www.bruker.comISDN: on request

http://www.bruker.de



http://www.bruker.com

http://www.bruker.com

1

Contents

Chapter 1 Introduction ........................................................................................................A-31.1 About this manual ................................................................................................A-31.2 Conventions ..........................................................................................................A-31.3 About dimensions .................................................................................................A-41.4 About digitally filtered Avance data ....................................................................A-51.5 Usage of acquisition commands in AU programs ................................................A-51.6 Starting commands from the XWIN-NMR menu ....................................................A-6

Chapter 2 XWIN-NMR parameters .......................................................................................A-72.1 About XWIN-NMR parameters ...............................................................................A-72.2 Parameter value types .........................................................................................A-102.3 Parameter files ....................................................................................................A-102.4 Acquisition (eda) parameters ..............................................................................A-112.5 Acquisition status (dpa) parameters ...................................................................A-522.6 Routing (edasp) parameters ................................................................................A-572.7 Lock (edlock) parameters ...................................................................................A-58

Chapter 3 Spectrometer configuration commands .........................................................A-61Chapter 4 Lock commands ..............................................................................................A-103Chapter 5 Shim commands ..............................................................................................A-119Chapter 6 Probehead commands ....................................................................................A-133Chapter 7 Parameter handling commands ....................................................................A-149Chapter 8 Pulse and AU program commands ...............................................................A-171Chapter 9 Acquisition commands ...................................................................................A-191Chapter 10 Temperature commands ................................................................................A-227Chapter 11 MAS/Solids commands ..................................................................................A-239Chapter 12 Rename and delete commands ......................................................................A-259Chapter 13 Miscellaneous ..................................................................................................A-267Chapter 14 NMR Suite files ...............................................................................................A-279Chapter 15 Bruker addresses ............................................................................................A-293

Command Index

Index

A-3

Chapter 1

Introduction

1.1 About this manual

This manual is a reference to XWIN-NMR acquisition or acquisition related commands and parameters. Every command is described on a separate page with its syntax and function as well and its main input/output files and parameters. Although file handling in XWIN-NMR is completely transparent to the user, it is sometimes useful to know which files are involved and where they reside. For example, if you have permission problems or if you want to process or interpret your data with third party software.

Some of the commands referred to in this manual are processing commands. They are all described in the Processing reference manual.

1.2 Conventions

Font conventionszg - commands to be entered on the command line are in courier bold italic

wobb-SW - commands to be clicked are in times bold italic

go=2 - pulse program statements are in courier small

A-4 Introduction

DONE

INDEX

INDEX

fid - filenames are in courier

contents - any contents of a text file is in courier small

name - any name which is not a filename is in times italic

File/directory conventions

<xwhome> - the XWIN-NMR home directory (default C\:Bruker or /u)

Header conventionsSYNTAX - only included if the command described requires arguments

USED IN AU PROGRAMS - only included if an AU macro exists for the com-mand described

Spectrometer naming conventionsThis manual is written for Avance spectrometers. Nevertheless, a large part of it is also valid for older spectrometers like AMX, ARX and ASX. Since the end of 1999, Bruker delivers a new type of Avance spectrometers that are specified in this manual as Avance-AQS. The conventional Avance spectrometers are spec-ified as Avance-AQX. You can easily find out which type of spectrometer you have by opening the cabinet door; one of the racks is named either AQS or AQX. Note that there are three types of Avance-AQX spectrometers: DMX, DRX or DPX. These specific names are used in this manual whenever a description only holds for one or two of them.

1.3 About dimensions

XWIN-NMR can acquire 1, 2 or 3 dimensional data. The dimensions of a dataset are indicated with the terms F3, F2 and F1 which are used as follows:

1D data

F1 - acquisition dimension

2D data:

F2 - acquisition or direct dimensionF1 - indirect dimension

3D data:

Introduction A-5

DONE

INDEX

INDEX

F3 - acquisition or direct dimensionF2 - indirect dimensionF1 - indirect dimension

In 3D processed data, F2 is always the second and F1 the third dimension. In 3D raw data, this order can be the same or reversed, depending on the value of AQSEQ (see the description of this acquisition parameter).

1.4 About digitally filtered Avance data

The first points of the raw data measured on an Avance spectrometer are called group delay. These points represent the delay caused by the digital filter and do not contain spectral information. However, they contain information about the digital filtering and are required for processing. The first couple of points of the group delay are always zero. The group delay only exists if digital filtering is actually used, i.e. if the acquisition parameter DIGMOD is set to digital.

1.5 Usage of acquisition commands in AU programs

Many acquisition commands described in this manual can also be used in AU pro-grams. The description of these commands contains an entry USAGE IN AU PROGRAMS. This means an AU macro is available which is usually the name of the command in capitalized letters. Note that ICON-NMR automation automatically calls acquisition AU programs. If, in this manual, the entry USAGE IN AU PRO-GRAMS is missing, no AU macro is available. Usually, such a command requires user interaction and it would not make sense to put it in an AU program. However, if you still want to use such a command in AU, you can do that with the XCMD macro which takes an XWIN-NMR command as argument. Examples are:

XCMD("eda")XCMD("setdef ackn no")

AU programs can be set up with the command edau.

Acquisition commands can also be used in an XWIN-NMR macro. These are scripts created with edmac containing a sequence of XWIN-NMR commands. The syntax of each line is simply an XWIN-NMR command (in lowercase letters) as it would be entered on the command line.

A-6 Introduction

DONE

INDEX

INDEX

1.6 Starting commands from the XWIN-NMR menu

This manual describes all acquisition commands as they can be entered on the command line. However, they can also be clicked from the XWIN-NMR popup menus. Most acquisition commands can be found under the Acquire menu. There, the corresponding command line commands are specified in square brackets.

A-7

Chapter 2

XWIN-NMR parameters

2.1 About XWIN-NMR parameters

XWIN-NMR parameters are divided in acquisition, processing, plot and output parameters. In this manual, we will mainly concern ourselves with acquisition parameters. Furthermore, we will discuss the acquisition related lock and prosol parameters.

The following terms will be used:

acquisition parameters

Parameters that must be set by the user, for example with eda, and that are in-terpreted by acquisition commands, for example zg.

acquisition status parameters

Parameters that are set by acquisition commands like zg. They represent the sta-tus of the raw data and can be viewed, for example with dpa. Some acquisition status parameters are used as input by processing commands.

lock parameters

Parameters that are used for locking the magnetic field. They can be set up with the edlock command and are interpreted when you lock in, either with the

A-8 XWIN-NMR parameters

DONE

INDEX

INDEX

lock command or from the BSMS keyboard.

prosol parameters

Probehead and solvent dependent parameters, mainly pulse lengths and power levels. They can be set up with the edprosol command. The getprosol command reads the prosol parameters and copies them to the corresponding ac-quisition parameters.

input parameters

Parameters that are interpreted by the commands described in this manual. They can be:

• acquisition parameters (input of, for example, zg)

• lock parameters (input of edlock, lock and lopo)

• prosol parameters (input of edprosol and getprosol)

output parameters

Parameters that are set or modified by commands described in this manual. They can be:

• acquisition status parameters (output of, for example, zg)

• lock parameters (output of edlock)

• prosol parameters (output of edprosol)

temporary parameters

Parameters that are not stored in parameters files and not interpreted directly by acquisition commands. They are related to other parameter that are directly in-terpreted by acquisition commands. If you change a temporary parameter, for example in eda, the related parameters will be automatically adjusted. An ex-ample of a temporary is AQ that is determined by the equation:

AQ = 2*TD/(SW*SFO1)

Acquisition parameters can be set with the parameter editor eda and acquisition status parameters can be viewed with dpa. Alternatively, each parameter can be set or viewed by entering its name in lowercase letters on the command line. Here are some examples of how you can set or view the parameter TD:

On a 1D dataset:

XWIN-NMR parameters A-9

DONE

INDEX

INDEX

• td - set the parameter TD

• 1s td - view the status parameter TD

On a 2D dataset:

• td - set the parameter TD in the F2 dimension (= direct dimension)

• 2 td - set the parameter TD in the F2 dimension (same as td)

• 1 td - set the parameter TD in the F1 dimension (= indirect dimension)

• 2s td - view the status parameter TD in the F2 dimension


On a 3D dataset:

• td - set the parameter TD in the F3 dimension (= direct dimension)

• 3 td - set the parameter TD in the F3 dimension (same as td)






Although status parameters are normally not changed by the user, a command like 1s td allows you to do that. This, however, would make the dataset inconsistent.

Before an acquisition has been performed, the acquisition status parameters of a dataset do not contain significant values. After the acquisition, they represent the status of the raw data.

Most acquisition status parameters are set to the same values as the corresponding acquisition parameters. In other words, the acquisition command has done what you told it to do. There are, however, some exceptions:

• when an acquisition was interrupted, the acquisition status parameters might not have been updated yet.

• some acquisition parameters are automatically adjusted by the acquisition command, e.g. RG and FW.

• the values of some parameters are a result of the acquisition. They cannot be set by the user (they do not appear as acquisition parameters) but they are


DONE

INDEX

INDEX

stored as acquisition status parameters. Examples are AQSEQ, YMAX_a and NC.

2.2 Parameter value types

With respect to the type of values they take, acquisition parameters can be divided into three groups:

• parameters taking integer values, e.g. NS, TD, DR

• parameters taking real (float or double) values, e.g. SW, O1, DE

• parameters using a predefined list of values, e.g. AQ_mod, DIGTYP

You can easily see to which group a parameter belongs from the parameter editor opened with the command eda. Note that the values of parameters which use a predefined list are stored in the parameter file as integers. The first value of the list is always stored as 0, the second value as 1 etc. Table 2.1 shows the values of the parameter AQ_mod as an example:

2.3 Parameter files

XWIN-NMR parameters are stored in various files in the dataset directory tree.

In a 1D dataset:

<du>/data/<user>/nmr/<name>/<expno>/

acqu - acquisition parametersacqus - acquisition status parameters

In a 2D dataset:


Parameter value Integer stored in the proc(s) file

qf 0

qsim 1

qseq 2

DQD 3

Table 2.1


DONE

INDEX

INDEX

acqu - F2 acquisition parametersacqu2 - F1 acquisition parametersacqus - F2 acquisition status parametersacqu2s - F1 acquisition status parameters

In a 3D dataset:


acqu - F3 acquisition parametersacqu2 - F2 acquisition parametersacqu3 - F1 acquisition parametersacqus - F3 acquisition status parametersacqu2s - F2 acquisition status parametersacqu3s - F1 acquisition status parameters

2.4 Acquisition (eda) parameters

This paragraph contains a list of all acquisition parameters with a description of their function. Most of them are interpreted by various acquisition commands like zg, go, ii, resume, gs, rga and pulsdisp. Some, however, are only inter-preted by specific commands which are then specified in the list below. Acquisi-tion parameters can be set with eda or by typing their names in lowercase letters on the command line.

AQ - acquisition time in seconds

• takes a float value

• temporary parameter calculated from the equation:

AQ = 2*TD/(SW*SFO1)

• AQ represents the time to acquire one scan. If you change AQ, TD is changed accordingly. The above equation holds for DIGTYP = SADC. Other digitizers require a 1-4 extra dwell times. This number is automati-cally detected from your digitizer by the acquisition software.

AMP[0-31] - amplitude of pulses

• takes float values in percent

• can be set from eda by clicking AMP ** Array **

• can also be set by entering amp0, amp1 etc. on the command line


DONE

INDEX

INDEX

• can also be set from gs by adjust-ing (FID display)

• can be only used on Avance-AQS spectrometers

• interpreted by the pulse program statements amp0, amp1, amp2 etc.

• The parameter AMP defines the percentage of the maximum pulse power. It can be used instead of or in addition to the parameter PL. The advantage of AMP is that the relation between AMP values and pulse power is more lin-ear than in the case of PL. Furthermore the pulse phases is more stable.

AQ_mod - acquisition mode

• takes one of the values qf, qsim, qseq, DQD

• can be set from eda or by entering aq_mod on the command line

• The values of AQ_mod have the following meaning:

qf = single channel detection.

qseq = quadrature detection in sequential mode. Two channels are used, whose reference phase differs by 90°. In the resulting fid, two successive data points have been acquired by different detectors with a time difference of DW.

qsim = quadrature detection in simultaneous mode. Two channels are used, whose reference phase differs by 90°. In the resulting fid, two successive data points have been acquired simultaneously by the two detectors. The time dif-ference between these points is 2* DW.

DQD = digital quadrature detection. Simultaneous mode that eliminates quad images and O1 spikes. AQ_mod can only be set to DQD when the parameter DIGMOD is set to digital or homodecoupling digital. When you set DIG-MOD to analog, AQ_mod automatically changes to qsim. Furthermore, DQD can only be used up to a certain spectral width as is shown in table 2.6. Above this value, acquisition commands automatically switch the acquisition mode to qsim. In that case, the acquisition parameter AQ_mod = DQD but the ac-quisition status parameter AQ_mod = qsim. Note that, in order to use DQD, your Avance spectrometer must be equipped with a DQD device on the RCU.

AUNM - name of an acquisition AU program

• takes a character array value


DONE

INDEX

INDEX

• can be set from eda or by entering aunm on the command line

• interpreted by xaua

• The command xaua executes the AU program specified by AUNM. Although this can be any AU program, AUNM is normally used to specify an AU program that performs an acquisition. For example, in several stand-ard parameter sets, AUNM is set to au_zg. The command xaua can be entered on the command line or called from AU program with its macro XAUA.

BF1 - BF8 - basic frequency for frequency channel f1 to f8

• take a double value (MHz)

• are automatically set when NUC1, NUC2 etc. are selected from edasp

• When you set up an experiment and define NUC1 in the routing table, BF1 is automatically read from the nucleus table. In the same way, BF2 is auto-matically read when NUC2 is defined etc. The routing table can be opened with edasp or by clicking NUCLEI in eda. The nucleus table is created with the command cf that can be executed by the NMR Superuser. This command prompts you for the 1H basic frequency and then automatically calculates the basic frequencies for all other nuclei. For each nucleus, cf sets the basic frequency such that the most common reference substance for that nucleus would resonate at about 0 ppm. If you want to change the nuclei table, you can do that with the command ednuc. This is, for example, nec-essary if you are using a different reference substance for a certain nucleus. Note, that if you execute cf and change the 1H basic frequency, you must click RESTORE in the nuclei table and execute cfbsms, after cf has fin-ished.

CNST[0-31] - array of constants used in pulse programs

• takes float values

• can be set from eda by clicking CNST ** Array **

• can also be set by entering cnst0, cnst1 etc. on the command line

• interpreted by the pulse program statements cnst0, cnst1, cnst2 etc.

• The values of the parameter array CNST can be used as constants in a pulse program. For example, the pulse program line:

"d2 = 1s/cnst2*2"


DONE

INDEX

INDEX

uses the value of CNST2 as a coupling constant. Note the difference between the pulse program statement cnst2 and the XWIN-NMR command cnst2. The latter is actually not a command but a way of setting the value of CNST[2].

CPDPRG1 - CPDPRG8 - names of CPD programs

• take a character string value

• can be set from eda by entering a name or by clicking the down arrow and then selecting a CPD program from the appearing list

• can also be set by entering cpdprg1, cpdprg2 etc. on the command line

• interpreted by the pulse program statements cpd1 - cpd8, cpds1- cpds8 and cpdngs1 - cpdngs8

• The values of CPDPRG1 - CPDPRG8 are the names of composite pulse decoupling (CPD) programs. The pulse program statements cpd1 executes the CPD program defined by CPDPRG1, cpd2 executes the CPD program defined by CPDPRG2 etc. In several Bruker CPD type parameter sets, the CPD program is specified by CPDPRG2 and executed on frequency channel f2. For example, the parameter set C13CPD contains the following settings:

CPDPRG2 = waltz16PULPROG = zgpg30

and the pulse program zgpg30 contains the following line:

d1 cpd2:f2

The statements cpd3 and cpd4 which execute the CPD programs specified by CPDPRG3 and CPDPRG4, respectively, are often used in 3D experi-ments. Note, however, that the cpd1 - cpd8 commands are equivalent and can be used to run any CPD program on any frequency channel.

cpds1 works like cpd1, except that it will execute the CPD program syn-chronously with the pulse program. This means cpds1 always starts the CPD program at the beginning, whereas cpd1 continues the CPD program where it was last stopped by the do statement. The difference between cpds2 and cpd2, cpds3 and cpd3 etc. is equivalent.

cpdng1 works like cpd1, except that the transmitter gate for channel f1 will not be opened. cpdngs1 works like cpds1, except that the transmitter gate for channel f1 will not be opened. For the channels f1, f2 ect. the statements cpdng2, cpdng3 etc are available. The cpdng* and cpdngs* statements are


DONE

INDEX

INDEX

available for Avance-AQX but not for the Avance-AQS.

The list of CPD programs which appears when you click the down arrow in eda, contains both Bruker and user defined CPD programs. Bruker CPD programs must be installed, once, with expinstall. You can set up your own CPD programs with the command edcpd.

D[0-31] - array of delays

• takes float values (seconds)

• can be set from eda by clicking D ** array **

• can also be set by entering d0, d1, d2 etc. on the command line

• interpreted by the pulse program statements d0 - d31, id0 - id31, dd0 - dd31, rd0 - rd31

• The pulse program statement d0 causes a delay of D0 seconds, d1 causes a delay of D1 seconds etc. In principle, all delays can be used for any purpose. In Bruker pulse programs, however, some conventions are followed. These are listed in the file Param.info that can be viewed with edpul. For exam-ple, D1 is used as a relaxation delay, D0 is used in combination with IN0 and ND0 as incrementable delay in 2D experiments. D0 and D10 are used as incrementable delays in 3D experiments. Note however, that all delays D1 - D31 are incrementable, not only D0 and D10. For more information click:

Help � Other topics � Writing pulse programs

DDR - digital digitizer resolution

• takes an integer value

• temporary parameter calculated according to the equation:

• cannot be set by the user

• DDR expresses the enhancement of the digitizer resolution by digital filter-ing. The total digitizer resolution, as defined by DR, is the sum of the hard-ware resolution (see table 2.2) and DDR.

DE - pre-scan delay

• takes a float value (microseconds)

• can be set from eda or by entering de on the command line

DDR DECIM( )log2

1+=


DONE

INDEX

INDEX

• DE is executed as a part of the go statement. On Avance-AQX spectrome-ters, DE consists of 5 pre-scan subdelays DEPA, DERX, DE1, DE2 and DEADC. These subdelays start simultaneously at the beginning of DE and after each subdelay a certain action is performed:

DEPA: the preamplifier is switched from transmit to observe mode (de-fault 2 µsec)

DERX: the receiver gate is opened (default 3 µsec)

DE1: the intermediate frequency (if required) is added to the frequency of the observe channel. This corresponds to the execution of the syrec statement (default 2 µsec). The intermediate frequency is only used for AQ_mod = DQD or, if your spectrometers has an RX22 receiver, for any value of AQ_mod.

DE2: the phase of the receiver is set to zero (default 1 µsec)

DEADC: the digitizer is enabled (default 4 µsec)

Note that sub-delay DE2 is used on Avance-AQX but not on Avance-AQS.

DE can be set from eda or from the command line. The subdelays can be set with the command edscon. Their maximum value is DE - 1 µsec. On Avance-AQS, the DE2 does not exist.

After DE, the digitizer starts to sample the data points.

For DIGMOD = analog, the parameter DE has a different purpose. It is used to achieve a near zero first order phase correction of the spectrum. In this case, DE does not consist of the above subdelays and is automatically adjust-ed when SW or DW are changed.

DECIM - decimation factor of the digital filter



• Avance spectrometers use the concept oversampling which means that the data points are sampled much faster than specified by DW. This results in a larger number of points than specified by the user; a multiple of TD. Before the data are written to disk, they are digitally filtered which reduces (deci-mates) their number to TD. The decimation factor is defined by the follow-ing equation:


DONE

INDEX

INDEX

DECIM = DW/DWOV

where DWOV is the oversampling dwell time. Note that DECIM can only take an integer value and DWOV must be greater than the minimum value for the current digitizer (see table 2.2). See also the acquisition status param-eter DECIM.

DIGMOD - digitizer mode

• takes one of the values analog, digital, homodecoupling-digital

• can be set from eda or by entering digmod on the command line

• In most standard parameter sets, DIGMOD is set to digital which means that oversampling and digital filtering is used. Oversampling means that the data points are sampled much faster that specified by DW. This results in a larger number of points than specified by the user; a multiple of TD. Before the data are written to disk, they are digitally filtered during which their number is reduced (decimated) to TD. For homodecoupling experiments on a Avance-AQX spectrometers, DIGMOD must be set to homodecoupling-dig-ital. Digital filtering is then switched on but the amount of oversampling is smaller (a larger DWOV is used). For homodecoupling experiments on Avance-AQS spectrometers, DIGMOD must be set to digital because the reduction of the oversampling rate is not necessary. For DIGMOD = analog, digital filtering is switched off and analog filters are used. In that case, your Avance spectrometer works like a AMX/ARX spectrometer. However, since only a limited number of analog filter values is available for Avance, setting DIGMOD to analog is not recommended.

DIGTYP - digitizer type

• takes one of the values listed in table 2.2.

• can be set from eda or by entering digtyp on the command line

• DIGTYP must be set to the value which corresponds to the digitizer in your spectrometer. If you enter digtyp on the command line, you can choose from all digitizers which are available for Bruker spectrometers. However, if you click on DIGTYP in eda, only the digitizer(s) which exist in your spec-trometer will appear. If you start your experiment with a Bruker standard parameter set (read with rpar), DIGTYP is usually set to the correct value. This is the value that was entered during the installation of the parameter sets with expinstall. If your spectrometer contains more than one digi-


DONE

INDEX

INDEX

tizer, you might want to change the default value of DIGTYP. Note that the SADC digitizer cannot be used for sequential acquisition (AQ_mod = qseq).

DQDMODE - sign of the frequency shift during digital quadrature detection

• takes one of the values add or subtract

• can be set from eda or by entering 1 dqdmode on the command line

• DQDMODE defines the frequency shift applied in Digital Quadrature Detection mode as positive (add) or negative (subtract).

DR - digitizer resolution


• DR is the sum of the hardware resolution (see table 2.2) and the digital digi-tizer resolution DDR. It is automatically set to the maximum resolution of the current digitizer (DIGTYP). Because Avance spectrometers use the prin-ciple of oversampling, this value can be higher than the resolution of the digitizer.

Usually, you want to use maximum resolution and keep this value of DR. In some cases, however, it is useful to set DR to a lower value. For example, if you want to acquire a large number of scans which might cause overflow for the maximum value of DR. However, to solve this problem, you can also set the parameter OVERFLW to check to halt the acquisition as soon as data overflow would occur.

DS - number of dummy scans


digtyp digitizer resolution(bit)

DWOV range(microseconds)

FADC (BC133) 12 0.05

HADC (HRD16) 16 2.5 - 5.0

SADC 16 3.325 - 6.65

HADC+ 16 2.5 - 5.0

SADC+ 16 3.325 - 6.65

IADC 16 0.1/0.05

Table 2.2


DONE

INDEX

INDEX

• interpreted by the pulse program statement go=n, gonp=n and rcyc=n

• can be set from eda or by entering ds on the command line

• Dummy scans are scans during which no fid is accumulated. Other than that, they are identical to normal scans, which means they take the same time (AQ) and perform phase cycling. Dummy scans are used to reach steady state conditions concerning T1 relaxation. This is necessary whenever the recycle delay of the experiment is shorter then 4 times the T1 value of the measured nucleus. Furthermore, they are used to establish a stable tempera-ture. This is especially important in decoupling and TOCSY experiments where the irradiation high power increases the sample temperature. Dummy scans are performed if DS > 0 and the pulse program contains a ze state-ment before the go=n or rcyc=n loop. If a zd is used instead of ze, dummy scans are omitted.

DSLIST - dataset list


• can be set from eda by entering a name in the DSLIST field or by clicking the down arrow and selecting a name from the appearing list. Note that this list also contains the entry EDIT CURRENT which allows you to edit the currently defined dataset list.

• can also be set by entering dslist on the command line

• interpreted by the pulse program statements wr #n, wr ##, ifp, dfp, rfp

• DSLIST defines the name of a variable dataset list. Such a list can be cre-ated with edlist � ds and has the following format:

sucrose 1 1 C:\ guest newsucrose 2 1 C:\ guest newfructose 1 1 D:\ guest old

where the option new/old is used to delete/keep a possibly existing dataset.

The list defined by DSLIST is interpreted by pulse program statements:

wr ## - stores the data in the dataset defined at the current list positionwr #n - stores the data in the dataset defined at list position nifp - increments the dataset list positiondfp -decrements the dataset list positionrfp - resets the dataset list position

where n = 1,2,3 etc.


DONE

INDEX

INDEX

DSPFIRM - firmware used for digital filtering

• takes one of the values sharp, medium, smooth, user_defined

• can be set from eda

• DSPFIRM defines the filter function used for digital filtering. This deter-mines the maximum spectral width that can be used. For high resolution experiments, DSPFIRM is usually set to sharp. The values medium and smooth are used for other applications. Note that smooth cannot be used for AQ_MOD = DQD. For DSPFIRM = user-defined, an external file is read from XWINNMRHOME/exp/stan/nmr/lists/DSPFIRM.

DW - dwell time


• can be set from eda or by entering dw on the command line

• temporary parameter, calculated from the equation:

DW=10e6/(2*SW*SFO1)

• The dwell time is the time between the acquisition of two successive data points. Although it is normally calculated from SW, you can also set dw. In that case, the spectral width is adjusted according to the equation:

SW=10e6/(2*(0.05+DW)*SFO1)

When you set DW, you will often notice that the value you enter is slightly adjusted. The reason is that, when oversampling is used, the relation

DW=DWOV*DECIM

must be fulfilled and DECIM can only take integer values.

DWOV - oversampling dwell time


• automatically set according to DIGTYP and DW

• has a minimum value which depends on the digitizer (see table 2.2)

• The parameter DWOV reflects the principle of oversampling. This is used when DIGMOD = digital and means that the data are sampled much faster than specified by the user. In other words, a data point is sampled every DWOV µs rather than every DW µs where DWOV is only a fraction of DW. DWOV is set to the minimum value that can be handled by the digitizer or


DONE

INDEX

INDEX

DSP-firmware (see table 2.2). Actually the value of DWOV is often a little above the minimum because the following relation must be fulfilled:

DWOV = DW/DECIM

Here, DECIM is the decimation factor that can only take integer values. For DIGMOD = analog (oversampling/digital filtering is switched off), DECIM is automatically set to 1 and DWOV is set to the value of DW.

EXP - experiment performed


• is set by ICON-NMR

• ICON-NMR sets EXP to the value of the parameter set that was used for the experiment.

FCUCHAN[0-8] - routing between logical frequency channels and FCU’s

• array of integer values

• can be set from eda but is normally set graphically from the edasp win-dow (see this command for more information)

• The values of FCUCHAN define the relation of the FCU’s to the logical fre-quency channels. For example, FCUCHAN[1] = 2 means that FCU 2 is used for logical channel f1.

FIDRES - FID resolution

• takes a float value (Hz)

• A temporary parameter calculated from the equation:

FIDRES=SW*SFO1/TD

• Although FIDRES is normally calculated from SW, you can also set FID-RES. In that case, TD is adjusted while SW remains the same. Note that the value that you enter for FIDRES if often adjusted a little. The reason is that TD is recalculated according to TD = SW*SFO1/FIDRES and rounded to the nearest power of two. FIDRES is then adjusted to fulfil the same equa-tion.

FnMODE - Acquisition mode of the indirect dimensions (2D and 3D)

• takes one of the values described below

• for 2D data, it can be set with eda or by entering 1 fnmode


DONE

INDEX

INDEX

• for 3D data, it can be set with eda or by entering 2 fnmode (F2 dimen-sion) or 1 fnmode (F1 dimension)

• interpreted by the pulse program statement mc

The parameter FnMODE is available in XWIN-NMR 3.0 and newer. It defines the acquisition mode of the indirect dimensions in a multi-dimensional ex-periment. The use of the mc statement and the FnMODE parameter, simpli-fies the switching of the acquisition mode and allows you to use the same pulse program for various experiments. For this reason, the number of Bruker pulse in XWIN-NMR 3.0 could be reduced compared to previous versions.

FnMODE can take the following values:

undefinedthis value must be used if the pulse program contains no mc statement.

QFsuccessive fids are acquired with incrementing time interval without changing any phase program. This corresponds to the mc clause F1QF or F2QF.

QSEQsuccessive fids will be acquired with incrementing time interval and phas-es 0 and 90 degrees. This corresponds to the mc clause F1PH or F2PH.

TPPI successive fids will be acquired with incrementing time interval and phas-es 0, 90, 180 and 270 degrees. This corresponds to the mc clause F1PH or F2PH.

Statessuccessive fids will be acquired incrementing the time interval after every second fid and phases 0 and 90 degrees. This corresponds to the mc clause F1PH or F2PH.

States-TPPIsuccessive fids will be acquired incrementing the time interval after every second fid and phases 0,90,180 and 270 degrees. This corresponds to the mc clause F1PH or F2PH.

Echo-Antiechospecial phase handling for gradient controlled experiments. This corre-sponds to the mc clause F1EA or F2EA.


DONE

INDEX

INDEX

For more information on the mc statement and the use of FNMODE click:


FQ1LIST - FQ8LIST - irradiation frequency lists

• take a character array value

• can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list

• can also be set by entering fq1list, fq2list etc. on the command line

• interpreted by the pulse program statements fq1 to fq8

• The parameters FQ1LIST to FQ8LIST define the names of frequency lists and are interpreted by the pulse program statement fq1 to fq8. For exam-ple, the first time fq1 is executed, the first value in the frequency list defined by FQ1LIST is read. The second time fq1 is executed, the second value in this list is read etc. At the end of the frequency list, the list position is set back to the first value. Note that fq1 can be executed multiple times because it occurs on several lines of the pulse program or because it occurs on a line that is part of a loop. In the same way fq2 reads the list defined by FQ2LIST etc. The fq1 to fq8 statements must be preceded with a delay and followed by the frequency channel on which the pulse will be executed, for example:

d1 fq2:f2

In Bruker pulse programs, fq1 is normally used on channel f1, and fq2 on channel f2 but any combination is allowed. The delay must be greater than 2 µs. The frequency lists can be created or modified with the command edlist.

FW - analog filter width


• can be set from eda or by entering fw on the command line

• FW defines the width of the analog filter. For DIGMOD = digital/homo-decoupling-digital, FW is automatically set for maximum oversampling. The value depends on the digitizer type, typically 125000 for HADC/2.

GP031 - gradient parameter table

• takes a list of real values (gradients) and character strings (filenames)

• can be set from eda by clicking GP031 edit


DONE

INDEX

INDEX

• the gradients are interpreted by pulse program statements gron0 - gron31 and :gp0 - :gp31

• the filenames are interpreted by pulse program statements :gp0 - :gp31

• XWIN-NMR allows you to use static gradients and shaped gradients. Static gradients have a constant strength during the time they are on. They are switched on by the pulse program statements gron0 - gron31. These read the gradient strength for each dimension from the GP031 table. The groff command switches the static gradients off. According to table 2.3, the pulse program section

d21 gron2d22d23 groff

would switch the X, Y and Z gradient on during the time D1+D2 with gradi-ent strengths 75.0, 75.0 and 75.0, respectively. The gradient strength is ex-pressed as a percentage of the maximum strength and runs from -100.0 to 100.0%. Static gradients do not use the Filename entry of the GP031 table.

Shaped gradients have a strength that varies in time. They are switched on by the pulse program statements gp0 - gp31. These interpret the Filename field of the gradient table. A file which is defined here contains a list of values be-tween -1 and 1. Each value represents the relative gradient strength for a giv-en time interval. They are multiplied with the values of GPX, GPY and GPZ to give the percentage of the maximum gradient strength for the respective dimension. According to the table 2.3, the statement p16:gp2 would switch on the X, Y and Z gradient on during the time P16 with gradient strengths 75.0, 75.0 and 75.0, respectively. The strength of each gradient would then vary in time according to the list of values in the file gradrec5m. When you click the down arrow to the right of each Filename field, a list of available files will appear. Such a list contains both Bruker and user defined gradient

Table 2.3

gradient parameters

Index GPX GPY GPZ Filename

0 0.0 0.0 50.0 SINE.100

1 -50.0 -50.0 -50.0 RECT.1

2 75.0 75.0 75.0 GRADREC5m


DONE

INDEX

INDEX

files. The former must be installed once with expinstall, with the option Install Library Gradient Files selected. The latter can be created with the Shape Tool (command stdisp). The gradient files reside in the directory:

XWINNMRHOME/exp/stan/nmr/lists/gp

The gradient parameters can also be set from the keyboard. For example, en-tering gpx2, gpy2, gpz2 allows you to set the gradient strength for the three respective dimensions. With gpnam2 you can set the shaped gradient file name.

GRDPROG - gradient program name

• takes an ascii string value

• interpreted by the pulse program statement ngrad

• Standard gradient programs are delivered with XWIN-NMR. They must be installed once, with the command expinstall with the option Install Library Gradient Files selected. The ngrad pulse program statement is mainly used on AMX/ARX spectrometers. On Avance systems, the gron/groff are normally used for gradient control. An exception is gradi-ent shimming, where the ngrad statement is used.

HDDUTY - homodecoupling duty cycle (in percent)


• can be set from eda or by entering hdduty on the command line

• HDDUTY describes the ratio between the time used for homodecoupling and the time used for actual signal detection.

HPMOD - routing between high power amplifiers and preamplifier modules



HPPRGN - high power preamplifier gain

• takes one of the values normal or plus

• Gain selection for spectrometers equipped with HPPR preamplifiers. By default, HPPRGN is set to normal. The value plus is only used for test pur-poses and should not be used for experiments.

INP[0-31] - array of increments for pulses P[0-31]


DONE

INDEX

INDEX

• takes double values (µsec)

• can be set from eda by clicking INP ** array **

• can also be set by entering inp0, inp1, inp2 etc. on the command line

• interpreted by the pulse program statements ipu0 - ipu31 and dpu0- du31

• The pulse program statement p0 executes a pulse with a length specified by P0. This length can be modified by the following pulse program statements:

ipu0 increments the pulse length by INP[0]dpu0 decrements the pulse length by INP[0]rpu0 resets the pulse length to the value of P[0]

In the same way, you can modify the length of the pulses executed by p1 to p31 with INP[1] to INP[31], respectively.

IN[0-31]- array of increments for delays D[0-31]

• takes double values (sec)

• can be set from eda by clicking IN ** array **

• can also be set by entering in0, in1, in2 etc. on the command line

• interpreted by the pulse program statements id0 - id31 and dd0- dd31

• The pulse program statement d0 causes a delay with a length specified by D[0]. This length can be modified by the following pulse program state-ments:

id0 - increments the delay by IN[0]dd0 - decrements the delay by IN[0]rd0 - resets the delay to the value of D[0]

In the same way, you can modify the length of the delays caused by d1 to d31 with IN[1] to IN[31], respectively.

In 2D dataset, IN[0] and ND[0] play a special role. In eda, they appear as the single parameters IN0 and ND0 in the F1 dimension. They are determined by the following equation:

SW(F1) = 1/(SFO1 * IN0 * ND0)

where IN0 is the spectral width and ND0 the number of occurrences of d0 in the pulse program. If you change IN0 or ND0, SW is automatically recalcu-lated. If you change SW, IN0 is recalculated and ND0 remains the same. You can set these parameters in eda or, from the command line, with:


DONE

INDEX

INDEX

in0 (same as 1 in0)nd0 (same as 1 nd0)1 sw

Note that IN0 and ND0 only exist in the F1 dimension but SW exists in F2 and F1.

In a 3D dataset, IN0 and ND0 play the same role in F1 indirect dimension as they do in the 2D dataset. F1, however, is the third dimension now. For the F2 indirect dimension F2, the parameters IN10 and ND10 are used. In 3D, the following equations hold:

SW(F1) = 1/(SFO1 * IN0 * ND0)SW(F2) = 1/(SFO1 * IN10 * ND10)

You can set these parameters in eda or, from the command line, with:

in0 (same as 1 in0)nd0 (same as 1 nd0)in10 (same as 2 in10)nd10 (same as 2 nd10)1 sw2 sw

Note that IN0 and ND0 only exist in F1, IN10 and ND10 only in F2 but SW exists in F3, F2 and F1.

L[0-31] - array of loop counters

• takes integer values

• can be set from eda by clicking L ** array **

• can also be set by entering l0, l1, l2 etc. on the command line

• interpreted by pulse program statements l0-l31, iu0-iu31, du0-du31 and ru0-ru31

• The parameters L[0] - L[31] are read by the pulse program statements l0 - l31. These are mainly used in loop structures like lo to x times l0 where x is a pulse program label; a number or a string which labels a previous line in the pulse program. An example of such a structure is:

4 (p1 ph1)d2..


DONE

INDEX

INDEX

lo to 4 times l3

The loop counter values can be varied as follows:

iu0 - iu31 increment the loop counter used l0 - l31 by 1.

du0 - du31 decrement the loop counter used l0 - l31 by 1.

Note that these increments and decrements only count during the execution of the current pulse program. They are not stored in the parameters L[0] - L[31]. Furthermore,

ru0 - ru31 reset the loop counter used l0 - l31 to L[0] - L[31]

The statements l0 - l31 are also used in if structures (conditions). Two sim-ple conditions are:

if "(l3 != 0)" : true if l3 is unequal zeroif "(l3 == 0)" : true if l3 equals zero

Further conditions are:

if "(l3 operand expression)"

where operand can be: ==, != , > , < , >= or <= and expression can be a number or an arithmetic expression built from pulses, delays and/or loop counters. The statements effected by a certain condition must be put between curly brackets. Furthermore, you can use the else structure for statements which must be executed if the condition is not true. An example is:

if "(l5 > 2)"{ p1 ph1

}else{

}

Note that the syntax of the conditional statements is similar to C language syntax. However, you cannot use the C "else if" statement.

LOCNUC - lock nucleus

• takes a character string value


DONE

INDEX

INDEX

• can be set from eda by entering a name in the LOCNUC field or by clicking the down arrow and selecting a nucleus from the appearing list

• can also be set by entering locnuc on the command line

• is interpreted by edlock, lock, lopo, lopoi, sref

• High resolution samples are usually locked on 2H or 19F. For these two nuclei, standard lock parameter files are delivered with XWIN-NMR. These can be edited with the command edlock.

MASR - MAS spin rate


• can be set from eda or by entering 1 masr

• can also be set with the commands mas or masr

• The MAS spin rate is usually set from the MAS control window which is opened with the command mas.

Note that entering masr on the command line does not merely set the param-eter MASR but starts the XWIN-NMR command masr.

NBL - number of blocks (of acquisition memory)


• interpreted by the pulse program statements st, st0, ze, zd, wr, if.

• The parameter NBL is used to acquire FID’s in multiple memory blocks, for example in NOE difference experiments. For NBL = 1 (the default value), one FID (NS averages) is written to disk at the end of the acquisition. For NBL > 1, multiple FIDs are acquired in the acquisition memory before these are written to disk. The st statement increments the memory pointer by TD in order to use the next block. The statement wr #0 will write NBL FIDs to disk. The following pulse program statements interpret NBL:

st - increment the memory pointer by TDwr - write NBL blocks to diskst0 - set the memory pointer to the position of the first FIDze, zd - clear the acquisition memory of all NBL blocksif - increment the file pointer in the raw data file by NBL*TDdf - decrement the file pointer in the raw data file by NBL*TDnbl - loop counter specifying the number of blocks

If TD is not a multiple of 256 (1024 bytes), successive FIDs will still begin


DONE

INDEX

INDEX

at 1024 byte memory boundaries. This is so for the FIDs in the acquisition memory as well as on disk. The size of the raw data file (ser) is therefore always a multiple of 1024 times NBL.

ND0 - number of delays D0


• temporary parameter

• only used in 2D and 3D datasets in the F1 dimension

• Number of d0 statements in the increment loops of a pulse program for 2D or 3D experiments. Used to calculate the spectral width in the F1 dimension according to:

SW = 1 / (SFO1 * ND0 * IN0)

N0 is set to 2, if the evolution time contains a 180 degree pulse (e.g. HMQC, HMBC, HSQC). Otherwise, it is set to 1 (e.g. NOESY, COSY,ROESY,TOC-SY).

ND10 - number of delays D10


• temporary parameter

• only used in 3D datasets in the F2 dimension

• Number of d10 commands in the increment loops of a pulse program for 3D experiments. Used to calculate the spectral width in the F2 dimension according to

SW = 1 / (SFO1 * ND10 * IN10)

ND10 is typically set to 2, if the evolution time contains a 180 degree pulse. Otherwise, it is set to 1. Usually this is described in the pulse program com-ment section.

NS - number of scans


• interpreted by the pulse program statement go=n, gonp=n and rcyc=n

• can be set from eda or by entering ns on the command line

• The pulse program statements go=n and rcyc=n loop NS times to the line which the label n. In Bruker pulse programs, the label n is usually 2. The


DONE

INDEX

INDEX

acquired data are accumulated in memory. After NS scans, the pulse pro-gram continues with the next statement which is often wr #0. This state-ment writes the accumulated data to disk.

After setting NS, you can calculate the resulting experiment time with the command expt. Then you can adjust NS such that the available time is prop-erly used. Alternatively, you can set NS to a high value and halt the experi-ment (with the command halt) when time is up (see also DS and OVERFLW).

NUC1 - NUC8 - nucleus for frequency channel f1 - f8

• take a value from a predefined list of nuclei

• can be set from eda by clicking NUCLEI

• can also be set from edasp (same as clicking NUCLEI in eda)

• The parameter NUC1 assigns a nucleus to the frequency channel f1, NUC2 assigns a nucleus to the frequency channel f2 etc. In most routine experi-ments, only NUC1, NUC2 and NUC3 are used. For example:

a 1D PROTON experiment without decoupling:

NUC1 = 1HNUC2 = offNUC3 = off

a 1D C13 experiment with 1H decoupling:

NUC1 = 13CNUC2 = 1HNUC3 = off

a 2D 1H experiment with 13C and 15N coupling:

NUC1 = 1HNUC2 = 13CNUC3 = 15N

In 2D datasets, NUC1 in the indirect dimension (F1) must be set explicitly by clicking F1-NUCLEI in eda (see the description of NUCLEI). In 3D datasets, this principle holds for both indirect dimensions, F2 and F1.

Because most Avance spectrometers are equipped with a maximum of four chan-nels, NUC5 to NUC8 are normally unused. Therefore, they appear at the end of the


DONE

INDEX

INDEX

eda table.

NUCLEI - set up nuclei and spectrometer routing

• appears in eda but is not a parameter

• opens the routing table (edasp) in 1D, 2D-F2 and 3D-F3

• In 1D and in the 2D and 3D acquisition (= direct) dimension, NUCLEI is not a parameter but a button to open the routing table. From this table, you can assign nuclei to the logical frequency channels of the spectrometer and define the amplifier routing. Clicking NUCLEI in eda is the same as enter-ing edasp on the command line. In the routing table, you can specify the nucleus or nuclei to be used for the experiment. For the f1 channel, you can click the NUC1 button and select a nucleus from the appearing list. The basic frequency, BF1, is automatically set. Then you can specify the fre-quency offset; OFSH1 for 1H or OFSX1 for X nuclei. The irradiation fre-quency SFO1 is automatically calculated as the sum of the basic frequency and frequency offset. Note that the parameters NUC1, BF1 and SFO1 also appear in eda but cannot be set from there. However, the frequency offset (OFSH1 or OFSX1) appears in eda as O1 and can be set from there. In a multi nuclear experiment, you can set up the parameters for channel f2, f3 etc. in the same way as described for f1.

The NUCLEI table also shows the spectrometer routing. The hardware ele-ments which have been detected when the spectrometer was configured (with cf or config) will appear in this list. When you select a nucleus for a cer-tain channel, the default routing is automatically set. Normally, this is okay. Only in very special cases it is useful to change it. The routing table consists of the following stages:

Channel---FCU---Amplifier---Swibox/I ---Swibox/O---Preamplifier

You can set up the routing by connecting an element from one stage to an el-ement of the next stage. A connection can be installed or removed by clicking the two elements involved. The routing must follow following rules:

a) Between the logical frequency channels and FCU’s any combination is allowed but only one to one.

b) An FCU can be connected to one amplifier only but an amplifier can be connected to multiple FCU’s. Furthermore, FCU1 can only be connected to the first three amplifiers. FCU2 can only be connected to the first four amplifiers.


DONE

INDEX

INDEX

c) The first four Amplifiers are automatically connected to Switchbox input in a fixed way. These connections cannot be changed.

d) Between the Switchbox input and Switchbox output, any connection is allowed but only one to one.

e) Between the Switchbox output and the Preamplifier modules, any con-nection is allowed but only one to one. Make sure that the cables are con-nected accordingly.

f) The output of the fifth and sixth amplifier must be connected directly to the Preamplifier modules. Any combination is allowed but only one to one and only to Preamplifier modules which are not connected to a Switchbox output.

Avance spectrometers which are used for solid state experiments usually con-tain high power amplifiers with two output stages:

• a low power output: typically 150 W for 1H or 300 W for X nuclei.

• a high power output: typically 1000 W for 1H or X nuclei

The second output appears as an extra stage in the routing table to the right of the switchbox. If you use the second output stage, the switchbox is always bypassed.

If you make a routing connection which is not allowed, you will get a mes-sage that it is illegal. You must remove it before you can save the routing ta-ble. Some connections are allowed but not recommended. In that case, you only get a warning.

Two extra switches are available to control the routing:

Preferred preamplifier toggle between selective and unselective Preamplifier module

Preferred output for 19F toggle between the 19F and X Switchbox output for 19F nucleus

Note that changing these settings changes the default routing. When you change these settings, you must click the DEFAULT button to make them ef-fective.

At the bottom of the NUCLEI table you will find the following buttons:

SAVE - save the parameters and routing and quit


DONE

INDEX

INDEX

SWITCH F1/F2 - exchange the F1 and F2 nucleus including the frequen-cy and frequency offset

SWITCH F1/F3 - exchange the F1 and F3 nucleus including the frequen-cy and frequency offset

DEFAULT - set the default amplifier routing for the current nuclei

CANCEL - quit without saving any changes

PARAM - shows the routing parameters

In a 2D dataset, NUCLEI has a different functions in the two dimensions. In F2, it works like in 1D experiments; it opens the routing table. In F1, it opens the nuclei list and allows you to select the nucleus for this dimension. The same principle holds for 3D data; in F3, NUCLEI opens the routing table, in F2 and F1 it opens the nuclei list.

The spectrometer routing is stored under the current dataset in the acquisition parameters FCUCHAN, RSEL, SWIBOX, PRECHAN and HPMOD (see the description of these parameters). These can be viewed by clicking the PAR-AM button in the routing table. Note that these parameters appear in eda and can be set from there. This, however is not very common as setting them from the routing table is much more convenient. In Bruker parameter sets (see rpar), the routing parameters have been set according to the configured hardware. This corresponds to the routing that will be set by clicking the de-fault button in the routing table.

O1 - O8 -irradiation frequency offset for frequency channel f1 - f8 in Hz

• take a double value (Hz)

• can be set from eda or by entering o1, o2 etc. on the command line

• can also be set from edasp by adjusting OFSH1, OFSX1, OFSH2 etc.

• can also be set from gs by adjusting Offset (FID display)

• O1 - O3 can be set by clicking utilities � O1, O2, O3 (spectrum display)

• O1 can be set by clicking utilities � sw-sfo1 (spectrum display)

• The parameter O1 represents the irradiation (carrier) frequency offset. It is the center of the spectral region to be acquired. O1 is related to the basic fre-quency and the carrier frequency according to:

O1 = SFO1 - BF1


DONE

INDEX

INDEX

The button sw-sfo1 in the utilities menu can be used if you are setting up your experiment from an existing spectrum. It sets O1 to the center of the currently displayed spectral region. The buttons O1, O2 and O3 put the cursor on the spectrum. You can then set the corresponding frequency offset by moving the mouse and clicking the middle mouse button on a certain position. Because most Avance spectrometers are equipped with a maximum of four channels, O5 to O8 are normally unused. Therefore, they appear at the end of the eda table. See also O1P - O8P.

O1P - O8P - irradiation frequency offset for frequency channel f1 - f8 in ppm

• take a double value (ppm)

• temporary parameters calculated from the equations:

O1P = O1/BF1O2P = O2/BF2etc.

• can be set from eda or by entering o1p, o2p etc. from the command line

• can be set by setting O1 - O8 (see these parameters)

• The parameter O1P represents the irradiation (carrier) frequency offset in ppm. Because chemical shift values are expressed in ppm, it is usually more convenient to set O1P rather than O1.

OVERFLW - data overflow check

• takes one of the values check or ignore (default is ignore)

• can be set from eda or by entering 1 overflw on the command line

• For OVERFLW = check, acquisition commands check for possible data overflow. Note that for OVERFLW = check, the performance of the spec-trometer RCU is decreased and the smallest possible dwell times cannot be used any more. Thus, if no overflow is to be expected, you should set OVERFLW to ignore.

P[0-31] - array of pulse lengths

• takes float values (µseconds)

• can be set from eda by clicking P ** array **

• can also be set by entering p0, p1, p2 etc. on the command line

• interpreted by the pulse program statements p0 - p31, ipu0 - ipu31, dpu0 - dpu31, rpu0 - rpu31


DONE

INDEX

INDEX

• The pulse program statement p0 executes a pulse of P[0] µseconds, p1 exe-cutes a pulse of P[1] µseconds etc. In principle, all pulses can be used for any purpose. In Bruker pulse programs, however, certain conventions are used. You can view the file that contains these conventions by entering the command edpul param.info

PARMODE - dimensionality of the raw data

• takes one of the values 1D, 2D or 3D

• interpreted by zg, rpar and by all processing commands which access raw data (see Processing Reference Manual)

• The parameter PARMODE defines the dimensionality of the raw data. 1D, 2D or 3D. It is interpreted by acquisition commands like zg and cross checked with the current pulse program. If the dimensionality of PAR-MODE and the pulse program are different, a warning will appear. If you want, you can still continue the acquisition.

PARMODE is also interpreted by processing commands which access the raw data. If, for example, you enter ft on a 1D dataset, it is simply Fourier transformed. If however, you enter ft on a 2D dataset, you are first prompted to enter the FID number you want to Fourier transform. Processing com-mands which access processed data, like abs, interpret the processing pa-rameter PPARMOD rather than the acquisition parameter PARMODE.

If you change PARMODE and set it to a lower dimension, the unnecessary files are deleted. For example, if you change it from 2D to 1D the files acqu2 and proc2 are deleted. However, you are warned before this actu-ally happens and you have the possibility of keeping all files.

If you enter rpar to read a parameter set with a different dimensionality then the current dataset, a warning about this will appear. If you click OK, the data files and superfluous parameters files will be deleted. However, if you enter rpar with two arguments on the command line, i.e. rpar <name> <type>, this will happen without a warning. The reason is that rpar is of-ten used in automation.

PHCOR[0-31] - array of correction angles for phase programs

• takes float values (degrees)

• can be set from eda by clicking PHCOR ** array **

• can also be set by entering phcor0, phcor1 etc. on the command line


DONE

INDEX

INDEX

• interpreted by the pulse program statements ph0:r - ph31:r

• The option :r after a phase program statement in a pulse program adds phase correction factor to the phase. For example, the statement:

p1 ph8:r

executes a pulse with the current phase from phase program ph8 plus the val-ue of PHCOR[8.] For ph8 = 0 1 2 3 and PHCOR[8] = 2, the phase cycle would be 2 92 182, 272 degrees.

PCPD[1-8] - array of CPD pulse lengths

• takes float values (µsec)

• can be set from eda by clicking PCPD ** array **

• can also be set by entering pcpd1, pcpd2 etc. on the command line

• interpreted by the CPD program command pcpd

• The PCPD parameters represent pulse lengths for CPD decoupling. They are interpreted by the CPD command pcpd. Which PCPD pulse is used depends on the frequency channel on which the CPD program runs. For example, the pulse program statement:

d1 cpd2:f2

runs the CPD program defined by CPDPRG2 on channel f2. Therefore, a pcpd command in this CPD program will execute a pulse of length PCPD[2].

Note that the element PCPD[0] exists but cannot be used because there is no channel that corresponds to it.

PH_ref - receiver phase correction

• takes a float value (degrees)

• interpreted by the pulse program statement go=n phxx:r

• PH_ref adds a value to the receiver phase. For example, the pulse program statement:

go=2 ph30:r

starts the acquisition with receiver phase:

ph30 + PH_ref

The AU program phtran calculates the value of PH_ref for a 2D dataset from the spectrum phase correction values of a 1D row (for more informa-


DONE

INDEX

INDEX

tion, type edau phtran and view the header of the AU program).

PL[0-31] - array of power levels

• takes float values (dB)

• can be set from eda by clicking PL ** Array **

• can also be set by entering pl0, pl1 etc. on the command line

• can also be set from the gs dialog window

• interpreted by the pulse program statements pl0, pl1, pl2 etc.

• The power levels PL[0] to PL[31] can be used to set the power for the fre-quency channels. The default power for channel fn is PL[n] (PL[1] for f1, PL[2] for f2 etc.) You can, however, explicitly assign a certain power level to a certain channel in the pulse program. For example, the pulse program statements:

pl1:f2pl3:f4

set the power of channel f2 to PL[1] and the power of channel f4 to PL[3] Note the difference between the pulse program statement pl1 and the com-mand pl1 entered on the XWIN-NMR command line. The latter is not really a command but simply a way to set the parameter PL[1]. The parameters PL[0-31] can also be used to set the power of hard or shaped pulses in CPD programs. For example, the CPD program statement:

p31:sp1:180 pl=pl1

sets the power of the shaped pulse sp1 to PL[1].

POWMOD - power mode

• takes one of the values low, high or linear

• POWMOD defines the power mode for spectrometers equipped with a high power accessory. The value linear is unused.

PRECHAN - routing between Switchbox outputs and Preamplifier modules



• The values of PRECHAN define the connection between the switchbox out-puts and the HPPR preamplifier modules. For example:


DONE

INDEX

INDEX

PRECHAN[1] = 0 : Output 1 is connected to HPPR module 0PRECHAN[3] = 1 : Output 3 is connected to HPPR module 1PRECHAN[1] = 2 : Output 1 is connected to HPPR module 2PRECHAN[2] = 3 : Output 2 is connected to HPPR module 3

For a standard HPPR configuration the module number correspond to the fol-lowing units: 0 = 2H, 1 = X-BB, 2=1H, 3=User-Box and 4 = 19F. For more information on the HPPR preamplifier see the BASH spectrometer documen-tation.

PROSOL - copy prosol parameters to corresponding acquisition parameters

• takes one of the values true or false

• is not a parameter but a push button in the eda dialog box

• Clicking the PROSOL button causes the prosol parameters to be read and copied to the corresponding acquisition parameters. As such, clicking PROSOL is equivalent to entering getprosol on the command line. The value of PROSOL indicates whether or not the prosol parameters have been copied, either by clicking PROSOL or running getprosol. Note that the getprosol command is automatically performed by ICON-NMR and but-tonnmr. Prosol parameters can be set up with the edprosol command. This is usually done once, after the installation of a new version of XWIN-NMR. The default relations between prosol and acquisition parameters are listed in table table 7.1.

PRGAIN - high power preamplifier gain

• takes one of the values low or high

• Gain selection for spectrometers equipped with MSL preamplifiers. Nor-mally, PRGAIN is set to high. The value low is only used for very strong NMR signals.

PULPROG - pulse program used for the acquisition


• can be set from eda by entering a name or by clicking the down arrow and selecting a pulse program from the appearing list. This list contains the entry EDIT CURRENT that allows you to edit the currently defined pulse program

• can also be set by entering pulprog on the command line

• also set by the command edcpul <name>


DONE

INDEX

INDEX

• Acquisition commands run the pulse program defined by PULPROG. If you set the pulse program in eda, you can click the down arrow to the right of the PULPROG field. A list of Bruker and user defined pulse programs will appear and you can click the one you need. Note that Bruker pulse programs must be installed once with expinstall. If you start your experiment by reading a standard parameter set (with rpar), PULPROG is usually set to the appropriate pulse program.

QNP - QNP nucleus selection

• takes one of the values 1,2 or 3

• If the current probehead is set to a QNP probe (see edhead), acquisition commands will interpret the parameter QNP to switch the probe to the cor-rect nucleus. QNP is a normally set with the AU program qnpset. Type edau qnpset to view this AU program.

RECCHAN[0-15] - array of receiver channels

• takes integer values

• can be set from eda by clicking RECCHAN ** Array **

• only used on Avance-AQS spectrometers

• RECCHAN enables the use of a different FCU than routed with edasp to generate the observe reference frequency. As such, the delay for the 22 MHz switching can be skipped.

RG - receiver gain


• RG controls the amplitude of the FID signal before it enters the digitizer. It is usually determined automatically with the command rga. This command performs an automatic determination of the optimum receiver gain. It runs several acquisitions with varying receiver gain until the maximum value is found that does not cause overflow. The parameter RG is then set to this value and depends on the receiver system of your spectrometer. If the RG value is already known from previous experiments, it can be set from eda or by entering rg on the command line. rg can also be set from gs.

RO - sample rotation frequency in Hz


• can be set from eda or by entering 1 ro on the command line


DONE

INDEX

INDEX

• interpreted by ro acqu

• The command ro acqu will set sample rotation to the value of RO. It will wait for 60 seconds and then check if the specified rate has been reached. If this is not the case, an error message is displayed.

Note that RO can be set by entering 1 ro on the command line but not by entering ro. The latter would start the command ro.

RSEL - routing between FCU’s and amplifiers


• can be set from eda but is usually set graphically from the edasp window (see this command for more information)

• The values of RSEL define the connections between the FCU’s and the amplifiers. For example:

RSEL[1] = 2 : FCU 1 is connected to amplifier 2 RSEL[2] = 0 : FCU1 is not connected to any amplifierRSEL[0] is unused

SEOUT - SE 451 receiver unit output to be used

• takes one of the values HR or BB

• This parameter is only used on DMX spectrometers with an SE451 receiver. This parameter is normally set to HR.

SFO1 - SFO8 - irradiation (carrier) frequencies for channels f1 to f8

• take a double value (MHz)

• are automatically calculated from the equation:

SFO1 = BF1 + O1SFO2 = BF2 + O2etc.

where O1, O2 etc. are set from edasp or eda

• can also be set with gs by adjusting Frequency (FID display)

• SFO1 can be set by clicking utilities � sw-sfo1 (spectrum display)

• The parameter SFO1 represents the irradiation (carrier) frequency for chan-nel f1. It is usually set from the by defining the nucleus and frequency offset for channel f1 in the routing table (opened with edasp).


DONE

INDEX

INDEX

SP07 - shaped pulse parameter table

• can be set from eda by clicking SP07 edit

• allows you to set power level, frequency offset, phase alignment and filename for 32 shaped pulses.

• interpreted by pulse program statements like sp0 - sp31

• When you open eda and click on SP07 edit, a list of shaped pulse parame-ters will appear as displayed in table 2.4.

The table has 32 entries (index 0-31) which are interpreted by the pulse pro-gram statements sp0 - sp31. These occur on pulse program lines like:

p1:sp2:f1

This line interprets entry 2 of the table and execute a Q3.1000 shaped pulse on channel f1 with length P1, Power 120.0, Offset 0.0 and Phase 0.55. When you click the down arrow to the right of a Filename entry, a list of available shape files will appear. This lists contains both Bruker and user defined shape files. The former must be installed once with expinstall. The latter can be created with the Shape Tool (command stdisp).

The SP07 entries are also available as acquisition parameters. They do not appear individually in eda but they can be set from the command line (see table 2.5)

They also appear as acquisition status parameters when you enter dpa.

SOLVENT - the sample solvent


Table 2.4

parameters for shaped pulses

Index Power[dB] Offset-Freq Phase-Align Filename

0 1.0 0.0 0.5 Gauss

1 20.0 0.0 0.5 Sinc1.1000

2 120.0 0.0 0.55 Q3.1000

3 .. .. .. ..


DONE

INDEX

INDEX

• can be set from eda by entering a name or by clicking the down arrow and selecting a solvent from the appearing list

• can also be set by entering solvent on the command line

• interpreted by getprosol and ICON-NMR automation

• also interpreted by lock -acqu, lopo and sref

• The parameter SOLVENT must be set to the name of the solvent used in the current sample. Some acquisition parameters like pulse length and power level are dependent on the probehead and the solvent. The command get-prosol interprets SOLVENT and PROBEHD and sets all dependent parameters accordingly. These parameters must be defined once, with edprosol, for all probeheads and solvents. After getprosol has been done, the eda parameter PROSOL is set to TRUE. In ICON-NMR automa-tion, getprosol is automatically performed after a standard experiment has been read.

SW - spectral width in ppm

• takes a double value (ppm)

• can be set from eda or by entering sw on the command line

• SW can be set by clicking utilities � sw-sfo1

• The spectral width should be set to such a value that all relevant peaks are expected to fall within that range. This means, for an unknown sample, SW should be set to a large value, like 50 ppm for a proton spectrum. The spec-tral width determines the dwell time according to the following equation:

DW=1/(2*SW*SFO1)

where DW is expressed in µsec.

When you enter a certain value for SW, you may notice that it is slightly ad-

Description Acquisition parameters Commands

power level SP[0-31] sp0 - sp31

frequency offset SPOFFS[0-31] spoffs0 - spoffs31

phase alignment SPOAL[0-31] spoal0 - spoal31

file name SPNAM[0-31] spnam0 - spnam31

Table 2.5


DONE

INDEX

INDEX

justed by XWIN-NMR. The reason is that the digitizer hardware can only han-dle discrete values of DW. For DIGMOD = digital/homodecoupling-digital, the maximum allowed spectral width depends on the digitizer, the acquisition mode and the DSP firmware (see table 2.6 and 2.7).

SW can also be set interactively by clicking the sw-sfo1 button in the 1D util-ities menu. This will set SW to the region currently displayed on the screen. It will also set SFO1 to the frequency of the center of that region. For 2D and 3D experiments, SW as it is described above corresponds to the width in the acquisition dimension. In the indirect dimensions, the spectral width are cal-culated from the parameters IN0, IN10, ND0, and ND10. In 2D, the follow-ing relations count:

SW(F1)=1/(SFO1*ND0*IN0)SWH(F1)= 1/(ND0*IN0)

In 3D, the following relations count:

SW(F2)=1/(SFO1*ND10*IN10) SWH(F2)= 1/(ND10*IN10)SW(F1)=1/(SFO1*ND0*IN0) SWH(F1)= 1/(ND0*IN0)

SWH - spectral width in Hz

• takes a double value

DSPFIRM

DIGTYP

Sharp Medium

FADC 25 100

HADC 25 25

HADC+ 25 25

HADC2 25 100

SADC 18.75 18.75

SADC+ 18.75 18.75

HRD16 25 25

IADC 25 100

Table 2.6 Maximum SW (kHz) for AQ_mod = DQD


DONE

INDEX

INDEX

• can be set from eda or by entering swh on the command line

• is related to SW according to the following equation:

SWH = SW * SFO1

During experiment setup, SW is usually defined and SWH is automatically calculated from it. The maximum values depend on the digitizer, the acquisi-tion mode and the DSP firmware as it is shown in table 2.6 and 2.7.

Note that SWH is stored in the parameter file acqu as SW_h.

SWIBOX - routing between Switchbox inputs and Switchbox outputs



• The values of SWIBOX define the connection between the swichbox inputs and switchbox outputs. For example, SWIBOX[1] = 3 means that Input 1 is connected Output 3.

TD - time domain; number of raw data points


• The parameter TD determines the number of raw data points to be acquired. A large value of TD enhances the spectrum resolution, but also increases the acquisition time AQ. TD is usually set to a power of 2, for example 64k for

DSPFIRM

DIFTYP

Sharp Medium Smooth

FADC 100 150 200

HADC 100 100 100

HADC+ 100 100 100

HADC2 100 150 200

SADC 75 75 75

SADC+ 75 75 75

HRD16 100 100 100

IADC 100 150 200

Table 2.7 Maximum SWH (kHz) for AQ_mod = qsim


DONE

INDEX

INDEX

a 1D spectrum. The FID resolution is related to the number of data points according to:

FIDRES=SW*SFO1/TD

In a 2D experiment, TD in the acquisition dimension (F2) has the same mean-ing as in 1D. In the indirect dimension (F1), it represents the number of in-crements. As such, it is interpreted by pulse program statements like:

lo to n times td1

In a 3D experiment, TD in the acquisition dimension (F3) has the same mean-ing as in 1D. In the indirect dimensions (F2 and F1), it represents the number of increments. As such, they are interpreted by statements like:

lo to n times td1 ; F1 loop in 2D or 3D experimentslo to n times td2 ; F2 loop in 3D experiments

In XWIN-NMR 3.0 and newer, the statement lo to n times td1 can be re-placed by the mc statement. Do not confuse this with the XWIN-NMR process-ing command mc that performs magnitude calculation.

TD0 - loop counter for multidimensional experiments


• interpreted by the pulse program statement td0

• TD0 is normally used as a loop counter for multiple 1D experiments that are measured under varying conditions (for example varying temperature or pressure) and that are stored as 2D data. Similarly, it can be used for multi-ple 2D experiments that are stored as 3D data.

TE - demand temperature on the temperature unit


• can be set from eda or by entering te on the command line

• interpreted by teset

• The command teset sets the temperature on the temperature unit to the value of TE. It be entered on the keyboard, or called from AU program with its macro TESET.

V9 - maximum variation of a delay

• takes a float value (between 0.0 and 100.0 percent)


DONE

INDEX

INDEX

• can be set from eda or by entering v9 on the command line

• interpreted by pulse program statements like d1:r, p1:r

• The pulse program statement d1 causes a delay D1. The statement d1:r, however, causes a delay D1 plus a random value. As such, the delay is a dif-ferent every time the statement d1:r is executed. The parameter V9 speci-fies, in percent, the maximum amount which is added to or subtracted from D1. As such, the effective delay varies between 0 and 2*D1. The :r option can be used for any of the statements d0 - d31 and p0 - p31 to vary D[0-31] and p[0-31], respectively. Note that the command gs ignores the :r option.

VALIST - variable amplitude (power) list


• can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list. This list contains the entry EDIT CURRENT that allows you to edit the currently defined amplitude list.

• can also be set by entering valist on the command line

• interpreted by user defined pulse program statements

• The parameter VALIST defines de name of variable amplitude (power) list. Such a list can be created with edlist va and has entries like:

-6.00.03.06.0

that represent attenuation values in dB.

The usage of a VA list is different from pulse and delays lists. You must de-fine the statement by which a VA list is accessed in the pulse program. Such a statement can have any name, for example the name vanam is used in the examples below. The suffixes .inc, .dex and .res can be used to incre-ment, decrement and reset the lists position, respectively. Furthermore, the caret operator (^) allows you to read a list value and increment the list posi-tion with one statement. The following pulse program entries illustrate the use of a variable amplitude list:

define list<power> vanam = <$VALIST>definition of the power list


DONE

INDEX

INDEX

d1 vanam:f2 vanam.dec set the power to the current value of the list and decrement the index

d1 vanam[2]:f3set the power to the second value of the list

"vanam.idx = vanam.idx + 3" increment the list index by 3

d1 vanam^:f4set power to the current value of the list increment the index

As an alternative to using a list defined by the parameter VALIST, you can explicitly define a variable amplitude (power) list filename or even the list values in the pulse program. The following examples illustrates such defini-tions:

define list<power> vanam=<my_filename>define list<power> vanam={10 30 50 70}

Note that the second definition does not require a list file. For more informa-tion on using variable amplitude lists click:


VCLIST - variable counter list


• can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list. This list contains the entry EDIT CURRENT that allows you to edit the currently defined counter list.

• can also be set by entering vclist on the command line

• interpreted by the pulse program statements lo to x times c, ivc, vcidx

• The parameter VCLIST defines de name of variable counter list. Such a list can be created with edlist � vc and has entries like:

4720

The currently defined list is interpreted by the pulse program statement:

lo to x times c


DONE

INDEX

INDEX

where x is a pulse program label and c is the value at the current position of the counter list. When this statement is executed for the first time, the current position is the first entry in the list. The position is incremented by the state-ment ivc.

VDLIST - variable delay list


• can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list. This list contains the entry EDIT CURRENT that allows you to edit the currently defined delay list.

• can also be set by entering vdlist on the command line

• interpreted by the pulse program statements vd, ivd and vdidx

• The parameter VDLIST defines de name of variable delay list. Such a list can be created with edlist � vd and has entries like:

10m50m2s

where m = milliseconds and s = seconds. The currently defined list is inter-preted by the pulse program statement vd that reads the delay value at the current position. When vd is executed for the first time, the current position is the first entry in the list. The position is not incremented by vd; this is done by the statement ivd. As such, vd is normally used in combination with ivd. The statement "vdidx=n" sets the index to position n in the list.

VPLIST - variable pulse list


• can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list. This list contains the entry EDIT CURRENT that allows you to edit the currently defined pulse list.

• can also be set by entering vplist on the command line

• interpreted by the pulse program statements vp, ivp and vpidx

• The parameter VDLIST defines de name of variable pulse list. Such a list can be created with edlist � vp and has entries like:

10u50m


DONE

INDEX

INDEX

2s

where u= microseconds, m = milliseconds and s = seconds. The currently de-fined list is interpreted by the pulse program statement vp that reads the pulse length value at the current position. When vp is executed for the first time, the current position is the first entry in the list. The position is not increment-ed by vp; this is done by the statement ivp. As such, vp is normally used in combination with ivp. The statement "vpidx=n" sets the index to position n in the list. A variable pulse list can only be used for hard pulses, not for shaped pulses or shaped gradients. As an alternative to a VP list, you can also specify a list of pulse values within the pulse program using a define state-ment. For more information on this topic click:


VTLIST - variable temperature list


• can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list. This list also contains the entry EDIT CURRENT which allows you to edit the currently defined temperature list.

• can also be set by entering vtlist on the command line

• interpreted by the AU program macros RVTLIST, VT, IVTLIST, DVTLIST

• The parameter VTLIST defines de name of variable temperature list. Such a list can be created with edlist � vt and has the following format:

300320340

where each entry is a temperature value in Kelvin.

Temperature lists are interpreted by the AU program macros:

RVTLIST - open the temperature list defined by VTLIST

VT - read the current value from the list and set it on the temperature unit

IVTLIST - increment the current position in the list to the next value

DVTLIST- decrement the current position in the list to the previous value

Note that temperature lists are only interpreted by AU program macros, not by


DONE

INDEX

INDEX

pulse program statements.

WBST - number of wobble steps

• takes an integer value between 256 and 4096 (default 256)

• interpreted by wobb

• The parameter WBST determines the number of steps (frequencies) used for tuning and matching a probehead (wobbling). A probehead is correctly tuned when the dip of the wobble curve is exactly at the center of the dis-play. Normally, the default value of WBST (256) is high enough for exact tuning. If necessary, you can set WBST to a higher value for a better resolu-tion. Note, however, that the maximum useful value is the screen resolution. Setting WBST to a higher value would not give you any advantage; it would only reduce the refresh rate. The command atma automatically calculates the optimum number of steps and does not interpret WBST 1.

WBSW - wobble sweep width

• takes a double value between 1 KHz and 4 MHz

• can be set from eda or by entering wbsw from on the command line

• can also be set by clicking Acquire � Observe fid window � wobb-SW

• interpreted by wobb

• The parameter WBSW sets the frequency range for tuning and matching a probehead (wobbling). The center of the wobble region is determined by SFO1. The command atma automatically calculates the optimum sweep width and does not interpret WBSW 1.

ZGOPTNS - acquisition (zg) options


• can be set from eda by entering zgoptns on the command line

• The parameter allows you to set an option to acquisition commands like zg and go. As an alternative, acquisition options can also be specified on the command line or in the pulse program. For example, the option DQF can be set in the following three ways:

by setting the parameter ZGOPTNS to DQF

1. During tuning/matching atma temporarily sets the parameters WBST and WBSW to the cal-culated values and then resets them to their original values.


DONE

INDEX

INDEX

by specifying the option as an argument, e.g.:

zg -DDQF

by defining the option in the pulse program, e.g.:

#define DQF

2.5 Acquisition status (dpa) parameters

This paragraph contains a list of all acquisition status parameters with a descrip-tion of their function. They are stored for each dataset in the file:


acqus - acquisition status parameters

and can be viewed with dpa. Some acquisition status parameters are interpreted by processing commands that work on raw data. Others are only stored as informa-tion for the user.

After an acquisition has finished, most acquisition status parameters have been set to the same value as the corresponding acquisition parameter. Sometimes, how-ever, this is different. For example:

• some parameters are continuously updated during the acquisition, e.g. NS, F1-TD (in 2D). When the acquisition is halted with halt, the current val-ues are stored as acquisition status parameters.

• some acquisition parameters are adjusted at the beginning of the acquisition, e.g. RG, FW, DR, SW. The modified values are stored as acquisition status parameters.

• the values of some parameters are a result of the acquisition. They cannot be set by the user (they do not appear as acquisition parameters) but they are stored as acquisition status parameters. Examples are AQSEQ, YMAX_a, LOCSHFT, NC.

The acquisition status parameters which are a result of or adjusted by the acquisi-tion are listed below.

AQ_mod - acquisition mode

• takes one of the values qf, qsim, qseq or DQD

• can be viewed from dpa or by entering 1s aq_mod on the command line


DONE

INDEX

INDEX

• Normally, the acquisition status parameter AQ_mod is set to the same value as the acquisition parameter AQ_mod. If, however, AQ_mod = DQD but DIGMOD = analog, zg performs an acquisition in simultaneous mode and set the status parameter AQ_mod to qsim. The same thing happens if your spectrometer is not equipped for DQD (see also the description of AQ_mod in chapter 2.4).

AQSEQ - 3D acquisition order

• only used in 3D datasets

• takes one of the values 321, 312

• can be viewed with dpa or by entering 1s aqseq on the command line

• interpreted by the processing command tf3

• AQSEQ describes the order in which the 3 dimensions have been acquired; F3-F2-F1 or F3-F1-F2. AQSEQ is automatically set according to the loop structure in the pulse program. A 3D pulse program usually contains a dou-ble nested loop with loop counters td1 and td2. If td1 is used in the inner loop and td2 in the outer loop, AQSEQ is set to 312. Otherwise it is set to 321.

AQSEQ is evaluated by a command which processes the raw data, usually tf3. The output data of this command are always in the order F3-F2-F1. If the acquisition status parameter AQSEQ is not set, tf3 evaluates the processing parameter AQORDER to determine the acquisition order.

DECIM - decimation factor of the digital filter


• can be viewed with dpa or by entering 1s decim on the command line

• interpreted by all processing commands which work on raw data.

• also interpreted by abs and apk

• Processing commands which work on the raw data like em or ft interpret the exact value of DECIM to account for the group delay. The commands abs and apk check whether DECIM is 1 (no oversampling) or greater than 1 (oversampling) to handle the so called smilies at the spectrum edges (see also the description of DECIM in chapter 2.4).

EXP - experiment performed



DONE

INDEX

INDEX

• ICON-NMR sets EXP to the value of the parameter set that was used for the experiment.

FnMODE - Acquisition mode in the indirect dimensions (2D and 3D)

• takes one of the values undefined, QF, QSEQ, TPPI, States, States-TPPI or Echo-Antiecho.

• can be viewed with dpa or by entering 1s fnmode (2D)

• interpreted by 2D and 3D processing commands that access raw data. These are usually xfb or xf2 for 2D data and tf3 for 3D data.

The parameter FnMODE is available in XWIN-NMR 3.0 and newer. It is inter-preted by processing commands to determine the Fourier transform mode in the indirect dimension(s). In XWIN-NMR 2.6 and older the processing param-eter MC2 is used for that purpose. Note that in XWIN-NMR 3.0 and newer, MC2 is still available. It is interpreted when the acquisition status parameter FnMODE has the value undefined.

DSPFVS - DSP firmware version

• takes an integer value between 11 and 15

• interpreted by processing commands that access raw data

• Different DSP firmware versions filter the raw data in a different way. It is set according to the acquisition parameter DSPFIRM. DSPFVS, together with DECIM, is interpreted to account for the group delay of digitally fil-tered data. DSPFVS must also be interpreted by third party software which processes digitally filtered Avance data.

LGAIN - loop gain; lock regulator gain

• is set to a value between -80 and 0 dB

• can be viewed with dpa or by entering 1s lgain

• LGAIN is set at the end of the acquisition to the loop gain value used at that moment, i.e. the value currently set on the BSMS unit. This usually, but not necessarily corresponds to the value of LGain in the edlock table. For example, if lock-in was performed with the command lock, the loop gain is first read from the edlock table and set on the BSMS unit. However, pressing the Autolock or Lock On/Off key on the BSMS keyboard per-forms lock-in without first reading the edlock table. Note in this respect that the current value of loop gain can also be changed from the BSMS key-


DONE

INDEX

INDEX

board (by pressing the two keys indicated with MENU) or by the command lgain.

LOCSHFT - lock shift

• takes one of the values true or false

• can be viewed with dpa or by entering 1s locshft

• The value of LOCSHFT indicates whether or not the sample was locked during the acquisition.

LTIME - loop time; lock regulator time

• is set to a value between 0.001 and 1.0 seconds

• can be viewed with dpa or by entering 1s ltime

• LTIME is a lock parameter (edlock) rather than an acquisition parameter (see the description of LGAIN above).

LFILTER - loop filter; lock regulator cut-off frequency of the lowpass filter

• is set to a value between 1 - 200 Hz

• can be viewed with dpa or by entering 1s lfilter

• LFILTER is a lock parameter (edlock) rather than an acquisition parame-ter (see the description of LGAIN above).

LOCKPOW - lock power

• is set to a value between -60 and 0 dB

• can be viewed with dpa or by entering 1s lockpow

• LOCKPOW is a lock parameter (edlock) rather than an acquisition parameter (see the description of LGAIN above).



• can be viewed with dpa or by entering 1s masr

• set by masr get

• The acquisition status parameters MASR is continuously updated when the MAS monitor (started with masrmon) is active. This, however, requires masrmon to be started from the current dataset. See also the description of MASR in chapter 2.4.

NC - normalization constant


DONE

INDEX

INDEX


• can be viewed with dpa or by entering 1s nc (1D), or 2s nc (2D)

• set by acquisition commands and by the processing commands genfid, genser and addfid

• interpreted by all processing commands that access raw data

• On Avance spectrometers, acquisition commands set NC to minus the value of DDR. Note that for DIGTYP = analog, DDR is 0 and, as such, NC is also 0. The processing commands mentioned above create pseudo raw and NC is set according to the input processed data.

PROBHD - probehead


• can be viewed with dpa or by entering 1s probhd on the command line

• PROBHD is set at the end of an acquisition to the current probehead as it was defined with edhead before the acquisition.

• LOCNUC

HOLDER - sample changer holder position


• can be viewed by entering 1s holder

• set by ICON-NMR

AUTOPOS - identification information from BEST-NMR rack or well-plate

• takes a character string value (A1-A12, B1-B12, ... , H1-H12)

• can be viewed by entering 1s autopos

• set by ICON-NMR

LOCKED - lock status during acquisition

• takes one of the values TRUE or FALSE

• can be viewed by entering 1s locked on the command line

• The status parameter LOCKED indicates whether or not the magnetic field was locked during the entire acquisition


DONE

INDEX

INDEX

2.6 Routing (edasp) parameters

The command edasp opens the routing table where you can select the nuclei and the spectrometer routing. When you select a nucleus for a certain frequency chan-nel, the basic frequency and the default routing for that channel are automatically set.

Parameters displayed in the routing table:

BF1 - basic frequencies for channel f1

same as the eda parameter BF1

NUC1 - nucleus for channel f1

same as the eda parameter NUC1

SFO1 - irradiation frequency for channel f1

same as the eda parameter SFO1

OFSX1 - irradiation frequency offset for the first X nucleus

OFSH1 - irradiation frequency offset for the first 1H

OFSF1 - irradiation frequency offset for the first F, 3H or Tl

OFSX2 - irradiation frequency offset for the second X nucleus

OFSH2 - irradiation frequency offset for the second 1H

OFSF2 - irradiation frequency offset for the second F, 3H or Tl

ect.

when defined for channel f1, these parameters correspond to O1 in eda

when defined for channel f2, these parameters correspond to O2 in eda

ect.

Note that the command edsp reads the values for OF* that were stored by the previous edsp or edasp command. It the latter was performed on dif-ferent dataset, the OF* values might differ from the corresponding O1, O2 etc. (see the description of edsp).


DONE

INDEX

INDEX

Parameters which can be viewed by clicking PARAM

FCUCHAN - connections between logical frequency channels and FCU’s

RSEL - connections between FCU’s and amplifiers

SWIBOX - connections between Switchbox inputs and Switchbox outputs

PRECHAN - connections between Switchbox outputs and Preamplifier modules

HPMOD - connections between high power amplifiers and Preamplifier mod-ules

Two switches to change the default routing

These parameters appear in the edasp dialog box under their descriptive names. Their two possible values are offered as radio buttons. They are not stored under the current dataset but in the file specpar.

DEFRSEL - Preferred preamplifier

takes one of the values selective or unselective

DEF19F - Preferred output for 19F

takes one of the values 19F or X

edasp stores its parameters under the current dataset in the file:


acqus - acquisition parameters

and the dataset independent file:

<xwhome>/conf/instr/<instrum>

specpar - edasp parameters

Note that the routing table can also be opened from the eda dialog box, by click-ing the NUCLEI button.

2.7 Lock (edlock) parameters

Lock parameters are used for locking the magnetic field and for referencing the spectrum. The lock-in procedure can be performed from the BSMS keyboard or with the command lock or lopo. Referencing the spectrum can be done with the


DONE

INDEX

INDEX

command sref.

Lock parameters used for locking the magnetic field:

Lockfreq - lock irradiation frequency

Field - Field value (H0)

BFREQ - Basic frequency

Solvent - Sample solvent

LPower - Lock power; the power used to irradiate the lock nucleus (-60 to 0 dB).

LGain - Loop gain; lock regulator gain (-80 to 0 dB)

LTime - Loop time; lock regulator time constant (0.001 to 1.0 seconds)

LFilt - Loop filter, lock regulator cut-off frequency of the lowpass filter (1 to 200 Hz)

LPhase - Lock phase; the phase of the lock signal

Nucleus - Observe nucleus

Distance - chemical shift of the lock nucleus (irradiation frequency offset)

Lock parameters used for referencing:

Ref. - chemical shift of the reference signal (default 0)

Width - width of the region where the reference signal is searched

RShift - reference shift for default calibration

The parameters LPower, LPhase, LGain, LTime and LFilt are probehead and sol-vent dependent. They are stored for each probehead and for each solvent sepa-rately in:

<xwhome>/conf/instr/<instrum>/prosol/<probeID>/<solvent>/

bsmspar - probehead dependent lock parameters

The other edlock parameters are only solvent dependent and are stored in the file:

<xwhome>/conf/instr/

2Hlock - probehead independent lock parameters


DONE

INDEX

INDEX

A-61

Chapter 3

Spectrometer configuration commands

This chapter describes all XWIN-NMR spectrometer configuration commands. These are commands which must be executed once after installing a new version of the NMR Suite.

A-62 Spectrometer configuration commands

DONE

INDEX

INDEX

cf

NAMEcf - configure the spectrometer

DESCRIPTIONThe command cf allows you to configure the spectrometer. It can be executed as a single command or as a part of the XWIN-NMR configuration suite (com-mand config).

cf should be executed:

• after installing a new version of the NMR Suite

• in case of spectrometer communication problems

It prompts you for the NMR Superuser password and then for various informa-tion about your spectrometer. The type of questions depend on whether you per-form a first time or a repeated configuration.

First time configuration:

cf will prompt you for the following information:

Enter new instrument name:

Enter a name for your spectrometer. The default name is spect. Note that the name that you enter is the hostname of the spectrometer internal CPU. As such, it must be different from the hostname of the PC or Workstation that controls the spectrometer. If you choose a hostname different from spect, you must specify this name in hosts file (see below).

What type of spectrometer?

Enter the type of your spectrometer. This question only appears on A*X and Avance-AQX. If you have an Avance-AQS, cf automatically detects your spectrometer type.

Basic 1H frequency (with offset O1=0) in MHz:

Enter the 1H frequency that corresponds to the strength of your magnet. Note that this frequency is typically, but not necessarily, one of the values 400.13, 500.13, 600,13 etc.

Spectrometer configuration commands A-63

DONE

INDEX

INDEX

After you have answered these questions, a window will appear that shows a list of all peripheral spectrometer hardware. For each unit, you have to specify the rs232 channel to which it is connected.

Next, the routing table will appear. Here, you can only set the connections be-tween Switchbox output and Preamplifier modules, or, if there is no Switch-box, between the Amplifiers and Preamplifier modules. If the routing table shows invalid routing lines, remove them by clicking CLEAR ALL. Then define new lines according to you hardware cable connections and click SAVE.

Next, the nuclei table will appear. Normally you can store this table as it is by clicking SAVE. If, however, you want to change the nuclei table, you can do that here. Note that you can also do that at a later time with the command ed-nuc.

Finally, an overview over the spectrometer configuration is shown. This al-lows you to check if your spectrometer hardware has been detected correctly. If some of the hardware is missing, please run cf again. If this does not change anything, run the spectrometer hardware checks.

A first time configuration is a configuration that is, for example, done on a new spectrometer, a new computer, a new disk or a new XWIN-NMR home directory. If, however, a new version of XWIN-NMR is installed in the same directory as a previous version, the configuration is still available. cf then runs a repeated configuration.

Repeated configuration:

cf will prompt you for the following information:

Configuration for <name>, change that (y/n) ?

where name is the spectrometer name which was specified the last time cf was executed. Hit Enter to keep this name or enter a new name.

All other questions are the same as the first time you ran cf. If the spectro-meter hardware has not changed, you can answer each question with Enter.

The window with the peripheral spectrometer hardware normally shows the correct serial ports. If, however, a unit could not be reached, it has the value no. In that case, you must specify its serial port number.

The nuclei table should be closed with SAVE.If, however, you have changed


DONE

INDEX

INDEX

the basic frequency, you must first click RESTORE.

Normally, the routing table can be closed by clicking CANCEL. If, however, any hardware cable connections between amplifiers and the HPPR preampli-fier have changed, you must make the corresponding changes in the routing ta-ble and close it with SAVE. Note that this step in cf corresponds to the command edasp setpreamp.

If you specify an instrument name different from spect, this name must be spec-ified in the hosts file. This file can be edited from the Windows Explorer or from a UNIX shell. It concerns the file:

/etc/hosts (under UNIX)C:\WINNT\SYSTEM32\DRIVERS\ETC\HOSTS (under Windows)

You must keep the name spect and append a white space plus the new instrument name, for example:

149.236.99.99 spect my_spectrometer

On most Avance-AQX spectrometers, a hardware list is needed. This is normally created during the installation of the spectrometer by the service engineer. The hardware list contains information about spectrometer components that cannot be detected by cf. When your spectrometer is extended with new hardware components, the hardware list must be updated accordingly. This must be done from the Windows Explorer or from a UNIX shell by editing the file:

/<xwhome>/conf/instr/<instrum>/hardware_list

After each modification of this file, cf must be executed.

If the hardware_list file does not exist, cf assumes a standard spectrome-ter. Some spectrometers are, indeed, equipped with standard components and do not need a hardware list. All possible hardware components are listed in the file:

/<xwhome>/conf/instr/hardware.exam

This file is not delivered with the NMR Suite nor is it interpreted by any com-mand. It can be created with the XWIN-NMR command cf makelist and can be used as a reference.

cf will automatically configure the sample changer and the temperature unit if these are specified in the hardware list. These unit will then appear in the list of hardware components where you can enter their rs232 channel number. For the sample changer, cf will prompt you with a few extra questions (see the com-


DONE

INDEX

INDEX

mand cfbacs). If the sample changer and temperature unit are not specified in the hardware list, they must be configured in a separate step with the commands cfbacs and cfte, respectively.

We strongly recommend to save the spectrometer configuration by copying the files uxnmr.par and hardware_list (see below) to floppy disk or CD and printing them out.

INPUT FILES

<xwhome>/exp/stan/nmr/form/

acqu.e.D - acquisition parameter format file (eda) for Avance

/<xwhome>/conf/instr/<instrum>/

hardware_list - hardware units that cannot be not detected by cf

OUTPUT FILES(also INPUT files for repeated configuration)


curinsthardware.exam - list of all hardware entries (output of cf makelist)


uxnmr.info - spectrometer configuration overviewuxnmr.par - spectrometer configurationnuclei - nuclei table

<xwhome>/conf/instr/<curinst>/rs232_device

acb - Amplifier control board rs232 channel bacs - Sample changer rs232 channelbsms - BSMS rs232 channellock - lock display rs232 channelpreemp - preemphasis rs232 channelpreamp1 - HPPR preamplifier rs232 channelpreamp2 - second HPPR preamplifier rs232 channel 1

preamp3 - third HPPR preamplifier rs232 channel 1

1. For multiple RCU spectrometers only.


DONE

INDEX

INDEX

rx22 - rx22 or rxc receiver unit rs232 channeltemp - temperature unit rs232 channel

SEE ALSOconfig, expinstall, cfte, cfbacs, cfmas, cfbpsu, cfmas


DONE

INDEX

INDEX

cfbacs

NAMEcfbacs - configure sample changer

DESCRIPTIONThe command cfbacs allows you to configure the sample changer. It first prompts you for the rs232 channel. Then it will ask you the following questions:

Should the sample changer control the lift?

with no as default answer.

Delay between SX and the next command [sec]?

where SX refers to the sample change. This delay is required for the sample to settle in the magnet. The first command after sample change is typically ro to switch the sample rotation on. The minimum value depends on the magnet type and lies, typically, between 10 and 30 seconds.

The command cfbacs can also be used if your spectrometer has no sample changer. This is, for example, useful for the automation setup with ICON-NMR on a separate workstation.

cfbacs can also be executed as a part of the XWIN-NMR configuration suite (command config). If your spectrometer uses a hardware list, and the sample changer is specified in that list, cfbacs can be skipped. The configuration of the sample changer is then executed by the command cf (see this command for more information on the hardware list).

INPUT AND OUTPUT FILES<xwhome>/conf/instr/<instrum>/rs232_device/

bacs - serial port for sample changer unit

<xwhome>/conf/instr/<instrum>/

bacs_params - number of holders in the sample changer

SEE ALSOconfig, cf, cfte, cfmas, cfbpsu


DONE

INDEX

INDEX

cfbpsu

NAMEcfbpsu - configure BPSU unit

DESCRIPTIONThe command cfbpsu allows set the rs232 channel for the BPSU unit. This unit is used for LC-NMR experiments.

cfbpsu can also be executed as a part of the XWIN-NMR configuration suite (command config).

INPUT AND OUTPUT FILES

<xwhome>/conf/instr/<instrum>/rs232_device/

bpsu - serial port for BPSU unit

SEE ALSOconfig, cf, cfte, cfmas, cfbacs


DONE

INDEX

INDEX

cfte

NAMEcfte - configure the temperature unit

DESCRIPTIONThe command cfte allows you to set the rs232 channel port for the temperature unit.

cfte can also be executed as a part of the XWIN-NMR configuration suite (com-mand config).



temp - rs232 channel for the temperature unit

SEE ALSOconfig, cf, cfbacs, cfmas, cfbpsu


DONE

INDEX

INDEX

compileall

NAMEcompileall - compile Bruker and User AU programs

DESCRIPTIONThe command compileall compiles all Bruker and User defined AU pro-grams. In order to compile Bruker AU programs, these must be installed first. This can be done with the command expinstall, with the option "Install Bruker library AU programs/modules" enabled.

For more information on AU programs please refer to the AU reference manual.

INPUT FILES<xwhome>/exp/stan/nmr/au/src/*

AU programs (source files)

OUTPUT FILES

<xwhome>/prog/au/bin/*

AU programs (executable binaries)

SEE ALSOexpinstall, cplbruk, cpluser, edau, xau, xaua, xaup, delau, renau


DONE

INDEX

INDEX

config

NAMEconfig - start the XWIN-NMR configuration suite

DESCRIPTIONThe command config starts the XWIN-NMR configuration suite. It opens a di-alog box which contains a list configuration steps. If this dialog box does not ap-pear, it is probably iconified. Just click its icon to open it. The config dialog box shows the following entries:

Spectrometer configuration [cf]

Temperature unit configuration [cfte]

Sample changer configuration [cfbacs]

Solvent table setup [edsolv]

Probehead table setup [edhead]

Solvent dependent parameter setup [edprosol]

Lock parameter setup [locnuc,edlock]

Configure MAS pneumatic unit [cfmas]

Configure BPSU unit for LC-NMR [cfbpsu]

Avance spectrometer constants [edscon]

Avance frequency routing [edsp]

Installation of standard experiments [expinstall]

For each entry the corresponding XWIN-NMR command is shown between square brackets. In order to start the configuration, do the following:

1. Check the entries which correspond to your spectrometer and uncheck the others. Note that [cf] should always be checked, even on a datasta-tion. In case of doubt, you can just leave the default selection.

2. Click the Start button. The first checked command is executed. Most commands prompt the user for input.

Note that the dialog box is sometimes HIDDEN behind the config win-


DONE

INDEX

INDEX

dow!

Wait until the command has finished.

3. Click the Continue button to execute the next command.

4. Click the Continue button to execute the next command.

5. ect.

6. When all checked commands have been executed, click Quit to leave the configuration suite.

The button Cancel allows you to start the entire configuration suite from the be-ginning, i.e. to rerun all checked commands.

INPUT FILES<xwhome>/prog/tcl/xwish3-scripts/

config - config Tcl/Tk source file

see also the OUTPUT FILES of the individual commands

OUTPUT FILESsee the OUTPUT FILES of the individual commands

SEE ALSOcf, cfte, cfbacs, edsolv, edhead, edprosol, locnuc, edlock, cfmas, cfbpsu, edscon, edsp, expinstall


DONE

INDEX

INDEX

cortab

NAMEcortab - correction table creation

DESCRIPTIONThe command cortab opens a window from which amplifier correction tables for acquisition can be created. These tables are used to correct the non-linearity of the pulse power level versus the pulse length. The amplifier linearization is performed in steps of 1 dB over the range between -6 and 73 dB and involves both amplitude linearization and phase correction. It requires that the amplifier output is connected to an external attenuator, which, in turn, is connected to the receiver input. The Cortab program will inform you how to connect the cables and to which value you must set the attenuator. The result of an amplifier line-arization is a correction table which is a list correction values for the pulse am-plitudes and phase values. An example of a correction table is shown in table 3.1.

Once a correction table exist, it is automatically used by acquisition commands like zg. If you want to check the accuracy of the amplifier linearization, Cortab allows you to do that by running a so called verification test. Amplifier lineari-zation and verification can be done in one Cortab experiment or in two separate experiments.

On Avance-AQS spectrometers, only amplifiers require a Cortab correction. On Avance-AQX spectrometers, however, both ASU’s (Amplitude Setting Unit) and amplifiers show non-linearity and require Cortab correction. Because the ASU appears earlier in the RF path, its correction table must be created first. The result of the ASU correction is then automatically used for the amplifier correc-tion.

Amplifier linearization can be performed in two possible ways:

• the amplifier output is connected to the external attenuator

• the amplifier output is connected to the preamplifier (as in an NMR experiment) and the preamplifier output is connected to the external attenuator

The output of these two possibilities is not exactly the same. In general, the sec-ond one, involving the preamplifier, is used because it is a better simulation of


DONE

INDEX

INDEX

the NMR experiment.

The cortab window allows you to setup the linearization experiments for var-ious nuclei, perform these experiments and view the results. A regular Cortab session involves the steps listed below. Each step is specified by its button in the main Cortab window.

Hardware Configuration (Xwin-nmr 3.0 and older)

Clicking this button makes the spectrometer configuration available for Cort-

AMP_POWER

# power in dB correction in %

-6.000 0.000

-5.000 -32.644

-4.000 -38.510

-3.000 -37.361

-2.000 -35.032

-1.000 -31.672

0.000 -29.128

1.000 -24.939

2.000 -22.977

.. ..

72.000 -0.008

AMP_PHASE

# power in DB correction in degree

-6.000 0.000

-5.000 -0.636

-4.000 0.622

.. ..

72.000 4.323

Table 3.1


DONE

INDEX

INDEX

ab. You must do this once, at the beginning of the first cortab session after the spectrometer configuration (as done with cf or config). It must only be repeated when your hardware has changed and cf has been executed again. In XWIN-NMR 3.1 and newer, this button does not appear because the spectrometer configuration is automatically read.

Experiment Setup

Clicking this button opens a dialog box where you can define one or more Cortab experiments. Cortab experiments should be defined for each nucleus that you intend to use in your NMR measurements. To set up an experiment, you must click an element from each field in the Setup window in the order listed below. Note that the experiment definition requires information about the spectrometer routing. This can be obtained by entering edasp on a data-set that contains a NMR experiment with the selected nucleus. Further note that a selection in one field may restrict the number of elements in the next field.

• NucleusSelect a nucleus

• ChannelSelect the channel (FCU) on which the chosen nucleus is observed

• AmpliSelect the amplifier to which the chosen FCU is routed.

• Pre AmpliSelect the preamplifier module to which the chosen amplifier is routed.

• FunctionsSelect the type of Cortab function (experiment) you want to do for the chosen nucleus.

On Avance-AQS spectrometers, the following functions are available:

BLA linearizationBLA verificationSGU verificationBLA Shape correction

On Avance-AQS spectrometers, most users only need the BLA lineari-zation. This function will create the correction tables that are required for the acquisition (see table 3.1). BLA verification is an optional func-


DONE

INDEX

INDEX

tion that allows to check the result of the BLA linearization. SGU veri-fication is only used to check the SGU hardware if a BLA linearization would fail. It does not use possible existing Cortab correction tables. The BLA shape correction is only needed for experiments that require high power shaped pulses.

On Avance-AQX spectrometers, Amplifier (BLA) and ASU (MULT and MOD) functions are available. They must be set up and executed in two separate series because they require different hardware connec-tions. First you must set up one series for the ASU functions, in the or-der MULT - MOD, and execute this series (see Start Experiment below). Then you can set up and execute a second series for the Ampli-fier linearization.

• Add ExperimentAdds the selected experiment (function) to the scheduled series. Instructions are displayed regarding the required hardware connections and the recommended value for the external attenuator is shown. Care-fully follow the outlined instructions.

In one Cortab series, you can add experiments for:

various nucleione nucleus with various routingslinearization and verification

You cannot, however, set an ASU correction and a BLA linearization in one series because they require different hardware connections.

• ReturnCloses the dialog box and returns to the main Cortab window

Start experiment

Clicking this button executes all experiments in the currently scheduled se-ries. They are performed in the order in which they appear in the list. Each linearization experiment involves the following steps:

• A receiver gain testdetermines the optimum receiver gain for the current experiment. If this is successful (S/N > 25 and the optimum receiver gain lies between 1 and 32), the experiment continues with the next step. If this is not successful, the experiment aborts and an information window will


DONE

INDEX

INDEX

appear telling what to do (usually adjust the external attenuator). Just follow the given instructions and restart the experiment.

• An attenuation test.performs an ASU attenuation test. This is normally successful and the experiment continues with the next step. If it is not successful, the experiment aborts; you might have an ASU hardware problem.

• The actual Cortab experiment, for example the BLA amplifier lineari-zation.

Note that you can add extra experiments during the execution of a Cortab ex-periment. They are simply appended to the end of the current series and exe-cuted as a part of that execution.

In principle, you are ready now. The correction table has been created and it will automatically be used by the acquisition. If, however, you want to check the Cortab result, you can do that with the View Results button as described below.

View Results

This button is only active when an experiment is selected in the Selection Desktop of the Cortab window. You can select an experiment by clicking an element in the fields Nucleus, Channel and Ampli. Clicking View Results will then open a window where the results of the selected experiment are shown. The window consists of the following fields:

• Date of the experimentsA list of dates at which Cortab experiments were performed.

• Name of the experimentsWhen a date is selected, a list of result filenames created at that date is displayed. For example:

Amp_Power_res - theoretical and experim. amplifier output voltage Amp_Phase_res - experimental amplifier phase valuesElec_Hard_Testfile - all Cortab results of the current date

When you click an entry, the contents of the corresponding file is shown. Note that, files like Amp_Power_res do not contain the cor-rection values but rather the theoretical and experimental values from which the correction values were calculated. In fact, the experimental values are the result of an acquisition after the calculation and applica-


DONE

INDEX

INDEX

tion of the correction values. The file Elec_Hard_Testfile con-tains the result of all Cortab experiments executed during the selected day.

• A data field where the contents of the selected file is displayed.

Furthermore, the following push buttons are available:

• Graphic windowopens a window with graphical representation of the Cortab result. At the time of this writing this was only available on UNIX systems.

• File print to printerSends the currently displayed result to the printer

• Back to main windowCloses the ’View Results’ window and returns to the main Cortab win-dow

Stop experiment

Clicking this button stops the current experiment and empties the list of scheduled series.

Scheduled series

Clicking this button opens a dialog box where the currently scheduled exper-iments are shown. The dialog box contains the following buttons:

• Read Series: reads previously saved set of experiments

• Save Series: saves the currently scheduled experiments to disk

• Remove All: removes all experiments from the scheduled list

• Remove: removes the selected experiment from the list

• Exit: exits the dialog box and returns to the main Cortab window

Nucleus List refresh

Clicking this button updates the nucleus list adding experiments that have been finished since Cortab has been started.

Cortab experiments use two spectrometer channels simultaneously:

• the pulse channel: selected by the user in the Cortab Experiment Setup, i.e. the channel that is routed to the amplifier (or ASU) that is being cor-rected.


DONE

INDEX

INDEX

• the observe channel: automatically selected by the Cortab program. If the pulse channel is f1, the observe channel is f2. Otherwise the observe channel is f1.

The selection of the observe channel is transparent to the user. An exception to this is the Avance-DPX spectrometer with ASU2/LOT. Here, only the f1 channel can be selected for observation. Cortab experiments on f1 (using f2 as the ob-serve channel) require a hardware modification. A description of this modifica-tion as well as various other Cortab details are described in the Cortab manual which can be opened from XWIN-NMR by clicking Help � Other topics � Cort-ab.

INPUT FILES<xwhome>/prog/app-defaults/

Cortab - cortab window resources

<xwhome>/exp/stan/nmr/au/src/

X* - cortab AU programs (sources)

<xwhome>/prog/au/bin/

X* - cortab AU programs (binaries)

<xwhome>/exp/stan/nmr/lists/pp.hwt

corcpdsDAV.* - cortab pulse programs for Avance-AQScorcpdsDMX.* - cortab pulse programs for Avance-AQX-DMXcorcpdsDRX.* - cortab pulse programs for Avance-AQX-DRXcorcpdsDPX.* - cortab pulse programs for Avance-AQX-DPX

<xwhome>/qtp/

Date.tmp - time and date of last Hardware configuration*.conf - hardware configurations (input of Experiment Setup)functions.AV - functions for Avance-AQS (input of Exper. Setup)functions.DRX - functions for Avance-AQX (input of Exper. Setup)

OUTPUT FILESOn Avance-AQX and Avance -AQS spectrometers

<xwhome>/conf/instr/<instrum>/cortab


DONE

INDEX

INDEX

amp<fcu no.>_<nucl.>_<ampl. RO> - amplifier correction tables

where RO is the router output number.

<xwhome>/qtp/<nucleus>/FCU<no>/<ampl. descr.>/<date>/

Amp_Power_res - theoretical and experimental amplifier output voltageAmp_Phase_res - experimental amplifier phase valuesAtt_verif_pha.<expno> - amplifier verification resultElec_Hard_Testfile - all Cortab results of the current date

*.conf - hardware configurations (output of Hardware Configuration)functions.* - Cortab functions (output of Hardware Configuration)

On Avance-AQX spectrometers only

<xwhome>/conf/instr/<instrum>/cortab

mma<fcu no.>_<nucl.>_<ampl. RO> - ASU correction tables

<xwhome>/qtp/<nucleus>/FCU<no>/<ampl. descr.>/<date>/

Mod_Power_res - theoretical and experimental ASU output voltageMod_Phase_res - experimental ASU phase valuesMult_Power_res - theoretical and experimental ASU output voltageMult_Phase_res - experimental ASU phase valuesAtt_verif_ampl.<expno> - MULT ampl. verification resultAtt_verif_pha.<expno> - MULT ampl. verification resultModverif_amp_<pln>.<expno> - MOD ampl. verification resultModverif_pha_<pln>.<expno> - MOD phase verification result

SEE ALSO

zg


DONE

INDEX

INDEX

cplbruk, cpluser

NAMEcplbruk - compile Bruker AU programscpluser - compile user defined AU programs

SYNTAX

cplbruk [<name> | all ]cpluser [<name> | all ]

DESCRIPTIONThe command cplbruk allows you to compile one or more Bruker AU pro-grams. Before you can use it, the command expinstall must have been ex-ecuted once, with the option "Install Bruker library AU programs/modules" enabled. Then you can use cplbruk in three different ways:

cplbruk <name> - compile the Bruker AU program <name>cplbruk all - compile all Bruker AU programscplbruk - a list of Bruker AU programs appears; click one to compile it

If you specify an argument, then it may contain wildcards; for example cplbruk a* compiles all Bruker AU programs which start with a.

The command cpluser works like cplbruk, except that it compiles user de-fined AU programs.

For more information on AU programs please refer to the AU reference manual.

INPUT FILES<xwhome>/exp/stan/nmr/au/src/*

AU programs (source files)

OUTPUT FILES<xwhome>/prog/au/bin/*

AU programs (executable files)


DONE

INDEX

INDEX

SEE ALSO

expinstall, compileall, edau, xau, xaua, xaup, delau, renau


DONE

INDEX

INDEX

ednuc

NAMEednuc - edit the nuclei table

DESCRIPTIONThe command ednuc opens the nuclei table. This table consists of two col-umns; the left column shows a list a nuclei, the right column the corresponding basic frequency.

Within the nuclei table, you can perform the following actions:

• Change the frequency of a nucleus by entering a new number in the right column.

• Delete a nucleus by clicking its entry in the left column

• Click ADD to add a nucleus. A list of all nuclei will appear and you can click the one you want to add.

• Click RESTORE to restore the original nuclei table. All changes you made will be undone. This must be done once, if you have changed the basic frequency with cf.

• Click SAVE to close the nuclei table, saving all changes.

• Click QUIT to close the nuclei table, discarding all changes

INPUT FILES<xwhome>/conf/instr/<instrum>/

nuclei - nuclei table

<xwhome>/exp/stan/nmr/lists/

nuclei.all - complete nuclei table (input of ADD and RESTORE)

OUTPUT FILES<xwhome>/conf/instr/<instrum>/



DONE

INDEX

INDEX

SEE ALSO

edsolv, edhead, edlock, edprosol


DONE

INDEX

INDEX

edprosol

NAMEedprosol - edit probehead and solvent dependent parameters

DESCRIPTIONThe command edprosol opens a dialog box in which you can set the probe-head and solvent dependent (prosol) parameters. This is typically done during the installation of your spectrometer for all probeheads and solvents you want to use. However, you can always run edprosol again at a later time to set the prosol parameters for additional probeheads and/or solvents.

Setting the prosol parameters involves the following steps:

1. Select the probehead, solvent(s) and nucleus:

• Probe nameBy default, the current probehead (as defined with edhead) is selected. Prosol parameters must be defined for each probehead separately.

• SolventThe default value is All. If you keep that value, the same prosol values will be stored for all solvents. If, however, you select a specific solvent, the prosol parameters will be stored for that solvent only.

• NucleusBy default, the nucleus of frequency channel f1 of the current dataset (NUC1) is selected. Prosol parameters must be set for each nucleus sepa-rately.

2. This step is optional. You can enter two comment lines; for example the conditions under which the pulses/power levels have been determined (fil-ters etc.).

3. Select the channels for which you want to define the parameters. You can do this by clicking one of the following radio buttons:

• F1+F2 : prosol parameters for the f1 and f2 frequency channel

• F3 : prosol parameters for the f3 frequency channel

• Global : a few prosol parameters that count for all frequency channels

By default, F1+F2 is checked. Most experiments only use channel f1 or f1


DONE

INDEX

INDEX

and f2. If you are using f3, you have to set the prosol parameters for this chan-nel as well. Note that f1, f2 and f3 refer to the logical frequency channels as you will see them in the routing table (edasp). They should not be confused with the terms that are used to indicate the dimensions of a 2D or 3D dataset.

4. Select the type of pulses that you want to set. For this purpose the following radio buttons are available at the bottom of the window:

• Standard hard pulsesshows a list of standard hard pulses and allows you to set their pulse lengths, power levels and mixing times (tocsy and roesy only)

• Standard soft pulsesshows a list of standard soft pulses and allows you to set their pulse lengths, power levels, phase alignments and shape files

By default, Standard hard pulses is checked which is sufficient for most ex-periments.

5. Set the pulse lengths and power levels for the selected frequency channel(s) and pulse type(s). You should start with the 90° hard pulse which must have been determined before you start edprosol. Then you can define all other pulses for the current channel. You can enter the pulse length and click the calc button to determined the corresponding power level. Alternatively, you can enter the power level and click the calc button to determine the corre-sponding pulse length. This, however, only works if the pulse length is set to 0 at the time calc is clicked. Note that the relation used by calc is deter-mined by the 90° hard pulse.

6. Save the prosol parameters by clicking the Save button at the bottom of the dialog box.

To the right of the Save button, you will find the following buttons:

• Copy to probeopens a list of all probeheads. You can select the probehead(s) for which you want to store the prosol parameters and then click one of the buttonsSave to all solvents or Save to selected solvents.

• Print screenList the currently selected prosol parameters on the printer

• ExitQuit the edprosol dialog box.


DONE

INDEX

INDEX

The edprosol dialog box provides a few additional options if you switch to expert mode. You can do that by clicking File � expert mode. Right above the parameter table, an arrow button will appear where you can select the amplifier connected to the currently selected channel. The default amplifier is normally correct. At the bottom if the window, two extra radio buttons will appear:

• user-defined hard pulsesshows a list of user-defined pulses and allows you to set their pulse length and power level.

• user-defined soft pulsesshows a list of user-defined pulses and allows you to set their pulse length and power level.

User defined hard and soft pulses require a separate (user defined) relations file. It can be setup from the Windows Explorer or from a UNIX shell.

The edprosol window allows you to set up a probehead dependent tune file. You can do that by clicking File � Edit tunefile. On first time execution, this command displays the example tune file that is delivered with XWIN-NMR. When you save the file, it is stored for the probehead that is currently defined in ed-prosol. Probehead dependent tune files are read by the command tune .sx.

The prosol parameters are interpreted by the getprosol command that copies them to the corresponding acquisition parameters. The default relations between prosol and acquisition parameters are listed in table 7.1. Note that getprosol is automatically performed as part of the ICON-NMR automation.

edprosol can also be executed as a part of the XWIN-NMR configuration suite (command config).

Note that the probehead and solvent dependent lock parameters are set with ed-lock.

The command edprosol replaces the commands prosol, solvloop and liprosol which were used in XWIN-NMR versions 2.6 and older.

INPUT FILES

<xwhome>/exp/stan/nmr/lists/group/

example_bsms - example tune file (input for first File � Edit tunefile)

<xwhome>/prog/tcl/xwish3_scripts


DONE

INDEX

INDEX

edprosol - Tcl/Tk script that is started by edprosol

<xwhome>/prog/tcl/libtix/prosol/lib/lists

routing - default spectrometer routing


If you select Solvent(s) All:

<xwhome>/conf/instr/<instrum>/prosol/<probeID>/

nucleus.channel.amplifier - standard prosol parametersparams - global (channel independent) prosol parameterstunefile - probe dependent tune file (input for File � Edit tunefile)

If you select a specific solvent:

<xwhome>/conf/instr/<instrum>/prosol/<probeID>/<solvent>

nucleus.channel.amplifier - standard prosol parametersparams - global (channel independent) prosol parameterstunefile - probe dependent tune file (input for File � Edit tunefile)

SEE ALSOgetprosol, edlock


DONE

INDEX

INDEX

edscon

NAMEedscon - edit spectrometer constants

DESCRIPTIONThe command edscon opens a dialog window, where you can set certain spec-trometer parameters (constants). The term constant refers to the fact that these parameters count for all datasets. edscon must be executed once as part of the spectrometer configuration. It can be entered from the command line or it can be executed as part of the config suite.

For Avance-AQX spectrometers, the upper part of the edscon window offers the following parameters:

BLKTR[1-8] - ASU and transmitter blanking preset time (default 3µ)BLKPA[1-5] - preamplifier blanking preset time (default 3µ)PHASPR[1-8] - phase switching preset time (default 3µ)SHAPPR[1-8] - shaped pulse calculation preset time (default 1.6µ)PHASP4[1-8] - 4PH modulator phase switching preset time (default 0.5µ)

They specify the time between a blanking or switching step and the beginning of the RF pulse. As such they are called preset parameters. For Avance-AQS, only BLKTR appears.

BLKTR and BLKPA are blanking preset times. The principle of blanking is used in the ASU (Amplitude Setting Unit), transmitter and preamplifier. This means they only allow RF signal to pass during the time they are blanked. Because of the finite switching time, blanking is triggered before the start of the RF pulse. The ASU and transmitter are blanked BLKTR µsec before the pulse, the pream-plifier is blanked BLKPA µsec before the pulse. All three units are unblanked (allow no further RF passing) at the end of the pulse.

PHASPR and PHASP4 are phase switch preset times. In many pulse programs, the phase of the RF pulse is switched after every scan, using a phase program (list). Because of the finite switching time, the phase switch is triggered before the start of the RF pulse. When a regular phase list like

ph1 = 0 90 180 270

is used, the phase is switched PHASPR µsec before the pulse. If, however, your


DONE

INDEX

INDEX

spectrometer is equipped with a 4-phase modulator, and a phase list like

ph1 = +x +y -x -y

is used, the phase is switched PHASP4 µsec before the pulse. Note that the de-fault value for PHASP4 (0.5µ) is much shorter than that for PHASPR (3µ). The reason is that the switching of phases created by the 4-phase modulator is much faster than that of regular phases.

SHAPPR is a shaped pulse preset time. A shaped pulse requires a short prepara-tion time, for example to reset a pointer to the beginning of the list of values that defines the shape. Note that after each shaped pulse, the pulse program must contain a minimum delay of 2 µsec on the respective channel.

Each preset parameter is an array of 16 elements but only elements 1 - 8 are used, corresponding to the maximum of 8 spectrometer channels. For BLKPA, only elements 1 - 5 are used, corresponding to the 5 preamplifier modules. For most high resolution experiments, you do not have to change the preset parameters and you can work with the default values that have been set during the installa-tion of your spectrometer. However, for some solids state experiments, it is often useful to use shorter values. We recommend the following settings:

• CRAMPS experiments (with f1 as the 1H observe channel):BLKTR[1] = 0.7 µs for DMX BLKTR[2] = 0.7 µs for DRX PHASPR[1] = 0.6 µs for DMX with TFH board (see uxnmr.info)

• CP experiments:PHASPR[2] = 1.7 µs PHASPR[2] = 0.6 µs for DMX with TFH board (see uxnmr.info)

• Back to back pulses: PHASPR[n] = 0.6 µs Avance-AQX with TFH board (see uxnmr.info) PHASPR[n] = 1.7 µs for DMX with TFX or DRX

For more information on this topic, click Help � Other topics � Solids Us-ers Manual

The use of the edscon preset parameters can be switched off by inserting the statement

preset off

at the beginning of a pulse program. This has the same effect as setting all ed-scon preset parameters to zero. In this case, the blanking and switching steps


DONE

INDEX

INDEX

described above occur at the beginning of the RF pulse. Nevertheless, you can enable the preset blanking for each individual channel, e.g.:

2µ gatepulse 1 ;enable blanking for channel f12µ gatepulse 1|2 ;enable blanking for channel f1 and f2

In this example, the blanking of ASU, transmitter and preamplifier is triggered 2 µsec before the RF pulse.

The edscon dialog box also shows the so called pre-scan subdelays. These are all part of the pre-scan delay DE. This is a hidden delay (it is not specified in the pulse program) but is automatically introduced by the go statement.

On Avance-AQX spectrometers, DE consists of 5 pre-scan subdelays DE1, DE2, DERX, DEADC and DEPA that all start simultaneously at the beginning of DE. At the end of each subdelay a certain action is performed:

DE1: the intermediate frequency (if required) is added to the frequency of the observe channel. This corresponds to the execution of the syrec statement (default 2 µsec). The intermediate frequency is only used for AQ_mod = DQD or, if your spectrometers has an RX22 receiver, for any value of AQ_mod.

DE2: the phase of the receiver is set to zero (default 1 µsec)

DERX: the receiver gate is opened (default 3 µsec)

DEADC: the digitizer is enabled (default 4 µsec)

DEPA: the preamplifier is switched from transmit to observe mode (default 2 µsec)

Normally, the default values, which have been set during the installation of your spectrometer, can be used. Each subdelay has a maximum of DE - 1 µsec. On Avance-AQS, the DE2 does not exist.

In most pulse programs, data sampling is performed by the go statement that au-tomatically triggers the actions mentioned above after the corresponding pre-scan subdelay. If, however, data sampling is performed by the adc statement, these actions must explicitly be specified in the pulse program. Each action can be performed by a statement with the same name, in lower case letters, as the corresponding pre-scan subdelay. For example, the receiver gate can be opened with the derx statement. You can type edpul zgadc to look at an example of a pulse program using the adc statement. For more information on this topic


DONE

INDEX

INDEX

click:


The prescan subdelays only play a role for digitally filtered data (DIGMOD = digital or digital homodecoupling). For DIGMOD = analog, the parameter DE has a different purpose. It is used to achieve a near zero first order phase correc-tion of the spectrum. In this case, it does not consist of subdelays.



scon - spectrometer constants

SEE ALSOcf, config


DONE

INDEX

INDEX

edsolv

NAMEedsolv - edit solvent table

DESCRIPTIONThe command edsolv opens the solvent table. This table contains one line for each solvent and shows the solvent name, a short description and a reference number. A typical line looks like:

Acetic - Acetic-Acid-D4 [02]

Furthermore, the solvent table contains the following buttons:

Add/Change

Appends an empty line in which you can add a new solvent. Please enter the solvent name, a short description (optionally) and a unique reference number. All existing lines are put in edit mode and can be changed. Make sure that each reference number is only used once.

Delete

Puts all lines in delete mode. If you click a entry now, it will be deleted.

Save

Closes the table, saving all changes.

Abort

Closes the table, discarding all changes.

Before you start an experiment, you must set the parameter SOLVENT to an entry from the solvent table. If you do this from eda, you can click the arrow button to the right of this parameter and select an entry from the solvent list.

edsolv can also be executed as a part of the XWIN-NMR configuration suite (command config).

INPUT FILES<xwhome>/exp/stan/nmr/lists/

solvents.all - complete Bruker solvent list (input for first edsolv)


DONE

INDEX

INDEX

solvents - user solvent list (input for second or later edsolv)

OUTPUT FILES<xwhome>/exp/stan/nmr/lists/

solvents - user solvent list

SEE ALSO

ednuc, edhead, edlock, edprosol


DONE

INDEX

INDEX

edsp

NAMEedsp - set up nuclei and spectrometer routing

DESCRIPTIONThe command edsp allows you to set up the nuclei and the spectrometer routing for the current experiment. edsp and edasp differ in only respect:

• edasp reads the irradiation frequencies offsets OFSH1, OFSX1, OFSX2 etc. from the current dataset.

• edsp reads the irradiation frequencies offsets OFSH1, OFSX1, OFSX2 etc. that were stored by the previous edsp or edasp.

A such, edsp allows you to transfer the frequency offset for a certain nucleus from one dataset to another. For example:

DATASET 1

rpar PROTON alledasp or edsp �

BF1 500.130 MHz NUC1SFO1 500.135 Mhz F1OFSH1 5000.00 Hz 1H

SAVE

DATASET 2

rpar PROTON alledsp �

BF1 125.757 MHz NUC1SFO1 125.758 Mhz F1OFSH1 1000.00 Hz 13C

BF1 500.130 MHz NUC2SFO1 500.135 Mhz F2OFSH1 5000.00 Hz 1H

The irradiation frequencies SFO1, SFO2 etc. are automatically adjusted to the corresponding frequency offsets.


DONE

INDEX

INDEX

The command edsp is also part of the spectrometer configuration. It must be executed only once, after the installation of XWIN-NMR. In this case, you only need to set the following switches:



and click SAVE to store them.

The Preferred preamplifier determines the default preamplifier module (selec-tive or unselective) for X-nuclei. The Preferred output for 19F determines the default output of the switchbox (X or 19F) for 19F.

edsp should be executed before expinstall which installs the standard pa-rameter sets. expinstall reads the values of Preferred preamplifier and Pre-ferred output for 19F, as they were set by edsp, and stores the default routing parameters accordingly.

INPUT AND OUTPUT PARAMETERS

see edasp

INPUT AND OUTPUT FILESsee edasp

SEE ALSOedasp, config, expinstall


DONE

INDEX

INDEX

expinstall

NAMEexpinstall - install pulse programs, AU programs, parameter sets etc.

DESCRIPTIONThe command expinstall installs pulse programs, AU programs, parameter sets and various other resources for spectrometer usage. It must be performed once after the installation of XWIN-NMR and after cf has been done. cf and ex-pinstall are typically performed as a part of the config configuration suite.

expinstall first prompts you for the NMR Superuser password. After it has been entered correctly, you see a list of spectrometer types. The spectrometer type you have defined with cf is highlighted. You can simply click Proceed, un-less you have a reason to choose a different type of spectrometer. expinstall will then offer you a list of tasks which can be selected or deselected. For routine spectroscopy, you can accept the default selection and click Proceed to continue. If the task Convert Standard Parameter Sets was selected, you will be prompted for some information about the spectrometer. Once this has been entered, ex-pinstall will start to execute the selected tasks. The full list of tasks is:

• Install pulse programs These are used for all experiments.

• Install Bruker library AU programsPerforming this task makes Bruker AU programs available for editing (edau) and compilation (xau or cplbruk).

• Recompile User AU programsAU programs must be (re)compiled after the installation of a new XWIN-NMR version because the installation has removed the AU binaries. expinstall only compiles User AU programs, not Bruker AU pro-grams. The latter can be compiled with compileall or cplbruk all.

• Install CPD programsThese are used for composite pulse decoupling experiments.

• Install gradient files These are used for gradient experiments.


DONE

INDEX

INDEX

• Install Library shape filesThese are used for selective excitation experiments.

• Convert standard parameter setsBruker standard parameter sets, as they are delivered with the NMR Suite, were prepared at various field strengths. expinstall converts them to your spectrometer frequency. This includes the parameters BFx, Ox, SFOx and SW as well as the offsets of the shaped pulses (parameter SPOFFS). Note that for 2D (3D), the SW in F1 (F2 and F1) is kept and the increment IN0 (IN0 and IN10) is adjusted.

• Install standard scaling region filesThese contain the regions in which the reference peak for vertical scaling is searched by commands like plot, li, lipp, pp*.

• Enable Define Statements in Pulse programsDefine statements are pulse program statements like:

;; d11=30m

at the beginning of a pulse program. In this form they are not active be-cause lines starting with a ’;’ character are treated as comment. expin-stall removes all occurrences ’;;’, thereby enabling the defined statements. Normal comment lines are not affected because they contain a single ’;’ only.

The NMR Suite is delivered with a set of pulse programs, CPD programs, gra-dient files, shape files and scaling region files for each spectrometer type (Avance, AMX, ARX etc.). expinstall installs the set which is needed on your spectrometer type.

If the task Convert Standard Parameter Sets is selected, expinstall will prompt you for the following information:

• Select type of digitizer :Click the digitizer that you want to store in the acquisition parameter DIGTYP in all parameter sets.

• Select acquisition mode :Click the acquisition mode that you want to store in the acquisition parameter AQ_mod in all parameter sets

• Enter default pre-scan-delay DE :Enter the value that you want to store in the acquisition parameter DE in all parameter sets. Normally, you can accept the default value.


DONE

INDEX

INDEX

• Select printer :Click the printer that you want to store in the output (edo) parameter CURPRIN in all parameter sets. This printer will be used by commands like lpa and lpp.

• Select plotter :Click the printer that you want to store in the output (edo) parameter CURPLOT in all parameter sets. This printer will be used by commands like view and plot.

• Enter paper format:Enter A4, A3, A or B. The entered value will effect various plot (edg) parameters like CX, CY and DHEI in all parameter sets. If you enter any value other than A4, A3, A or B, the file:

<xwhome>/exp/stan/nmr/lists/plotconvpar

is interpreted for the paper format 1. This file is delivered with XWIN-NMR and you can change it for your purpose from the Windows Explorer or from a UNIX shell.

INPUT PARAMETERS

If the task Convert standard parameter sets is selected, expinstall uses the following input parameters:

set by the user with edsp :

DEFRSEL - preferred preamplifier (default routing)DEF19F - preferred output for 19F (default routing)

from the parameter sets as delivered with XWIN-NMR:

BF1 - BF4 - basic frequencies for channel f1 to f4SFO1- SFO4 - irradiation (carrier) frequencies for channels f1 to f4IN0 - increment for delay D0 (2D and 3D parameter sets only)IN10 - increment for delay D10 (3D parameter sets only)SW - spectral width in ppmSPOFFS[0-7] - shaped pulse frequency offset

1. Note that the file plotconvpar.A3 is used for A3 and B and plotconvpar.A4 for A4 and A.


DONE

INDEX

INDEX

OUTPUT PARAMETERS

If the task Convert standard parameter sets is selected, expinstall stores the following parameters in the parameter sets:

BF1 - BF4 - basic frequencies for channel f1 to f4SFO1- SFO4 - irradiation (carrier) frequencies for channels f1 to f4SF - spectral reference frequencyIN0 - increment for delay D0 (2D and 3D parameter sets only)IN10 - increment for delay D10 (3D parameter sets only)SW - spectral width in ppmSPOFFS[0-7] - shaped pulse frequency offsetDIGTYP - digitizer typeDR - digital resolutionDIGMOD - digitizer modeDECIM - decimation factor of the digital filterDE - prescan delayFCUCHAN - routing between logical frequency channels and FCU’sRSEL - routing between FCU’s and amplifiers SWIBOX - routing between Switchbox inputs and Switchbox outputsPRECHAN - routing between Switchbox outputs and Preamplifier modulesHPMOD - routing between high power amplifiers and Preamplifier modules

INPUT FILES<xwhome>/conf/instr/<instrum>/specpar - routing parameters

<xwhome>/prog/au/src.exam/* - Bruker AU programs (source files)

<xwhome>/exp/stan/nmr/au/src/* - AU programs (source files)

<xwhome>/exp/stan/nmr/par.avance/* - Bruker parameter sets for Avance

<xwhome>/exp/stan/nmr/par.300/* - Bruker parameter sets for A*X

<xwhome>/exp/stan/nmr/pp.dexam/* - pulse programs for Avance

<xwhome>/exp/stan/nmr/pp.exam/* - pulse programs for AMX

<xwhome>/exp/stan/nmr/cpd.dexam/* - CPD programs for Avance

<xwhome>/exp/stan/nmr/cpd.exam/* - CPD programs for AMX

<xwhome>/exp/stan/nmr/gp.dexam/* - gradient programs for Avance


DONE

INDEX

INDEX

<xwhome>/exp/stan/nmr/gp.exam/* - gradient programs for AMX

<xwhome>/exp/stan/nmr/wave.dexam/* - shape files for Avance

<xwhome>/exp/stan/nmr/wave.exam/* - shape files for AMX

<xwhome>/exp/stan/nmr/scl.exam/* - scaling region files for Avance/AMX

Depending on the spectrometer type and/or application, expinstall uses various other input folders/files using the extensions:

.rexam - high resolution on ARX

.solids - solid state on AMX/ASX

.imag - micro imaging on AMX

.tomo - tomography

.dsolids - solid state on Avance

.dimag - micro imaging on Avance

OUTPUT FILES

<xwhome>/exp/stan/nmr/au/src/* - Bruker AU programs (source files)

<xwhome>/prog/au/bin/* - AU programs (binary executables)

<xwhome>/exp/stan/nmr/par/* - parameter sets for your spectrometer

<xwhome>/exp/stan/nmr/pp/* - pulse programs for your spectrometer

<xwhome>/exp/stan/nmr/cpd/* - CPD programs for your spectrometer

<xwhome>/exp/stan/nmr/gp/* - CPD programs for your spectrometer

<xwhome>/exp/stan/nmr/wave/* - shape files for your spectrometer

<xwhome>/exp/stan/nmr/scl/* - scaling region files for your spectrometer

SEE ALSOcf, config, cplbruk, cpluser, compileall, rpar, wpar

A-103

Chapter 4

Lock commands

This chapter describes the commands which are involved in locking the magnetic field. Avance spectrometers use a digital lock that is provided by the BSMS unit. Locking the magnetic field is done by measuring the signal of a lock nucleus and adjusting the magnetic field whenever its frequency shifts. Common lock nuclei are 2H and 19F.

A-104 Lock commands

DONE

INDEX

INDEX

edlock

NAMEedlock - edit the lock table

DESCRIPTIONThe command edlock opens the lock table; a dialog box in which the lock pa-rameters can be set. It must be executed once for each probehead and each lock nucleus. The lock parameters can be determined from the BSMS keyboard or from the BSMS display (command bsmsdisp).

Before you run edlock, you must define the current probehead with the com-mand edhead. Furthermore, you must define the lock nucleus by setting the pa-rameter LOCNUC. This can be done with eda or by entering locnuc on the command line. In most experiments, the lock nucleus is deuterium. As such, LOCNUC is set to 2H in most Bruker standard parameter sets (see rpar).

When edlock is executed for the first time on a certain probehead, a default lock table, which is delivered with XWIN-NMR, is opened.

The first line of the lock table shows the lock nucleus and the current probehead. The second line shows the lock frequency, the field value (H0) and the basic spectrometer frequency. The latter must be specified when the spectrometer is configured with cf or config. The lock frequency is automatically calculated from the basic spectrometer frequency.

The main part of the lock table shows a list of solvents and, for each solvent, the lock parameters. Most lock parameters are used for locking the magnetic field during the acquisition. Others, however, are used for referencing the spectrum after the acquisition has finished.

Lock parameters used to lock the magnetic field:

LPower - Lock power; power used to irradiate the lock nucleus (-60 to 0 dB)

LGain - Loop gain; lock regulator gain (-80 to 0 dB)

LTime - Loop time; lock regulator time constant (0.001 - 1.0 seconds)

LFilt - Loop filter, lock regulator cut-off frequency of the lowpass filter (1 - 200 Hz)

Lock commands A-105

DONE

INDEX

INDEX

LPhase - Lock phase; the phase of the lock signal

Nucleus - Observe nucleus

Distance - Chemical shift of the lock nucleus (irradiation frequency offset)

These parameters are interpreted by the commands lock and lopo.

Lock parameters used to reference the spectrum (sref):

Ref. - chemical shift of the reference signal (default 0)

Width - width of the region where the reference signal is searched

RShift - reference shift for default calibration

At the bottom of the lock table, the following buttons/fields are available:

• SAVE - saves the current values and closes the dialog box

• BSMS-FIELD - reads the field value (H0) from the BSMS unit

• NUCLEUS - selects an observe nucleus for each solvent. This is equiva-lent to clicking the Nucl. button on one solvent and selecting new.

• NEW SOLVENT - adds an extra solvent entry to the list. The currently selected (highlighted) entry is copied and the solvent field can be edited. If no entry is highlighted at the time you click NEW SOLVENT, the last entry will be copied.

• DELETE - switches to delete mode. If you click on a solvent now, its entry will be deleted. If you click on the nucleus button of a particular solvent, the currently selected nucleus is deleted for that solvent.

• ABORT - closes the lock table discarding all changes

• LOADSTAN - loads the standard (default) values for all parameters. These are the same values which are loaded when edlock is executed for the first time.

• +/- POWER - in this field you can enter the number that should be added to the lock power (LPower) of all solvents. A positive number increases the lock power, a negative number decreases it.

• LIST - prints the lock parameters on the device specified by the edo parameter CURPRIN

• COPY_VALUE automatically copies the value of the selected parameter to all solvents

A-106 Lock commands

DONE

INDEX

INDEX

The loop gain, loop time and loop filter can also be set with the XWIN-NMR com-mands lgain, ltime and lfilter, respectively. Furthermore, they can also be set from the BSMS keyboard menu. This menu can be entered by simultane-ously pressing the two keys indicated with MENU.

The lock phase can be adjusted from the BSMS keyboard while observing the lock sweep on the lock display (lockdisp).

Note the difference between loop gain which can be set in edlock or with lgain and lock gain which can be set on the BSMS keyboard.

The AU program loopadj, automatically optimizes the lock phase, lock gain, loop gain, loop filter and loop time. Note that loopadj optimizes these param-eters for best long-term stability, but not for best lineshape, resolution or homo-geneity (for more information type edau loopadj and look at the header of the AU program).

The Lock Power should be about 6 dB below the value where the lock signal starts to saturate. Saturation can be observed by increasing the lock power while observing the lock signal. When the signal no longer increases or starts to de-crease, it is saturated.

In ICON-NMR automation, the lock parameters are read from the lock table and used as they are.

edlock can also be executed as a part of the XWIN-NMR configuration suite (command config).

For information on how to determine the lock parameters click Help � Other topics � Avance Users Guide. Furthermore, you can refer to the spectrometer hardware documentation. It can be viewed by inserting the BASH CDROM and clicking Help � Other topics � BASH spectrometer documentation.

INPUT AND OUTPUT PARAMETERSsee DESCRIPTION above


2Hlock - 2H lock parameters (input for first edlock on current probe)19Flock - 19F lock parameters (input for first edlock on current probe)

Lock commands A-107

DONE

INDEX

INDEX



2Hlock - 2H lock parameters19Flock - 19F lock parameters


bsmspar - solvent and probehead dependent lock parameters

SEE ALSO lock, lopo, lopoi, edhead, lockdisp, lgain, ltime, lfilter

A-108 Lock commands

DONE

INDEX

INDEX

lgain, ltime, lfilter

NAMElgain - set the lock regulator loop gainltime - set the lock regulator loop time lfilter - set the lock regulator loop filter

SYNTAXlgain [<gain>]ltime [<time>]lfilter [<filter>]

DESCRIPTIONThe command lgain allows you to set the loop gain, a lock regulator parame-ter. It takes one argument; a loop gain value between -80 and 0 dB. This value is only used when the lock-in process is done from the BSMS keyboard; i.e. by pressing Lock On/Off or Autolock. When lock-in is done with the XWIN-NMR command lock, the loop gain is set to the edlock parameter LGain.

ltime and lfilter work like lgain, except that they set the regulator pa-rameters loop time and loop filter, respectively.

The AU program loopadj automatically optimizes lock gain, lock phase, loop time, loop gain and loop filter.

The regulator (loop) parameters can also be set from the BSMS keyboard menu. This can be opened by simultaneously pressing the two keys indicated with MENU.

For information on how to determine the lock parameters click Help � Other topics � Avance Users Guide. Furthermore, you can refer to the spectrometer hardware documentation. This can be viewed by inserting the BASH CDROM and clicking Help � Other topics � BASH spectrometer documentation.

USAGE IN AU PROGAMSLTIME(value)

LGAIN(value)

LFILTER(value)

Lock commands A-109

DONE

INDEX

INDEX

SEE ALSO

lock, lopo, lopoi, edlock

A-110 Lock commands

DONE

INDEX

INDEX

lock

NAMElock - lock the magnetic field

SYNTAXlock [ <solvent> | -acqu | -noauto ]

DESCRIPTION

The command lock performs the automatic lock-in procedure. It takes one ar-gument and can be used in the following ways:

lockopens a dialog box with a list of solvents. When you select a solvent, it reads the lock parameters for that solvent and performs an auto lock-in accordingly.

lock <solvent>reads the lock parameters for the specified solvent and performs an auto lock-in accordingly.

lock -acqureads the lock parameters for the solvent defined by the acquisition parameter SOLVENT and perform an auto lock-in accordingly.

lock -noautoreads the lock parameters for the solvent defined by the acquisition parameter SOLVENT and performs a lock-in (not auto lock-in, see below) procedure.

lock reads the lock parameters from the lock table which has been set up with the command edlock. (see table 4.1).

The auto lock-in procedure involves the following steps:

1. Irradiation of the lock nucleus with frequency Lock Freq + Distance

2. Acquisition of the reflected lock signal

3. Fourier transform and magnitude calculation of the acquired FID

4. Determination of the position of the lock signal in the spectrum.

5. Adjusting the Field such that the lock signal is exactly on resonance.

6. Optimization the lock power, lock gain and lock phase.

Lock commands A-111

DONE

INDEX

INDEX

Note that the lock irradiation frequency (Lockfreq + Distance) is solvent depend-ent. The value of Distance is the chemical shift of the lock nucleus in the current solvent. As such, the irradiation frequency is approximately on resonance and lock needs to make only minimum field adjustments. The advantage of this procedure is that the signal of the reference substance (e.g. TMS) appears at ap-proximately the same position for each solvent. This is the difference between the BSMS lock unit and the SCM lock unit. The latter use the same lock irradi-ation frequency for each solvent and shift the field to put the lock signal on res-onance. Note that all Avance and some AMX/ARX spectrometers are equipped with a BSMS unit.

The command lock -noauto simply reads the lock parameters and performs a lock-in accordingly. It does not adjust the field, nor does it optimize any lock parameters. lock -noauto is typically used for samples with multiple lock nuclei or mixed solvents. The advantage is that you are sure to lock-in on the lock nucleus that corresponds to the lock parameters whereas the auto lock-in procedure would use the nucleus with the strongest signal.

lock reads the regulator parameters loop gain, loop time and loop filter from the lock table. However, these are only used after lock-in has been performed, i.e. after the lock command has finished. During the lock-in process fixed reg-ulator values are used.

Lock parameters Description BSMS keyboard

Field field (H0) FIELD

LPower lock power LOCK POWER

LPhase lock phase LOCK PHASE

- lock gain LOCK GAIN

LGain loop gain Menu a

Ltime loop time Menu a

LFilt loop filter Menu a

Distance lock frequency shift LOCK SHIFT

Table 4.1

a. Can be modified by simultaneously pressing the buttons indicated with MENU

A-112 Lock commands

DONE

INDEX

INDEX

The lock signal can be viewed in the lock display window which can be opened with the command lockdisp (see the description of this command).

The lock-in procedure can also be performed from the BSMS keyboard by press-ing the Autolock or Lock On/Off key. In that case the lock parameter values that are currently stored on the BSMS unit are used. These can be modified from the BSMS keyboard as indicated in table 4.1 or read from the lock table with the command lopo. As such,

lopo � Autolock is equivalent to lock

lopo � Lock On/Off is equivalent to lock -noauto

For information on how to determine the lock parameters click Help � Other topics � Avance Users Guide. Furthermore, you can refer to the spectrometer hardware documentation. This can be viewed by inserting the BASH CDROM and clicking Help � Other topics � BASH spectrometer documentation.

INPUT PARAMETERSset by the user with eda or by typing solvent etc.:

SOLVENT - sample solvent (input for lock -acqu and lock -auto)LOCNUC - lock nucleus

set by the user with edlock:

see table 4.1

INPUT FILES


acqu - acquisition parameters


probehead - current probehead as defined with edhead


2Hlock - lock table for nucleus 2H19Flock - lock table for nucleus 19F



Lock commands A-113

DONE

INDEX

INDEX

USAGE IN AU PROGRAMS

LOCKexecutes the command lock -acqu.

SEE ALSOedlock, lopo, lopoi, lockdisp, lgain, ltime, lfilter

A-114 Lock commands

DONE

INDEX

INDEX

lockdisp

NAMElockdisp - open the lock display window

DESCRIPTIONThe command lockdisp opens the lock display window in which the lock sig-nal is shown. The lock signal is the NMR signal of the lock nucleus which is usu-ally 2H.

The lock display can be used in two different ways:

1. When the field is unlocked. In this case the lock frequency is swept and lock signal shows a pattern of wiggles with a maximum intensity at the resonance frequency. This pattern can be used to set the field value and lock phase. The field value can be adjusted from the BSMS keyboard until the maximum lock signal lies at the center of the lock display window. The lock phase can be adjusted until the intensity is about the same on both sides of the center.

2. When the field is locked.In this case the lock frequency is kept at the resonance position of the lock nucleus and is only adjusted in responds to changes in the magnetic field. The lock signal is a horizontal line in the upper part of the lock dis-play window. Furthermore, the position of this line can be used for shim-ming the magnet. When the homogeneity of the field improves, the lock signal increases, i.e. the line moves upward.

The lock display window offers the following buttons:

mode toggles between two color modes. In one mode, forward and backward sweep have the same color. In the other mode, they have different colors.

store prompts you for a filename to save the current size and position of the lock display window and the current grid and mode settings. The read button al-lows you to read previously saved settings. lockdisp starts up with stand-ard settings which are stored in the file default. If this file does not exist, it start up with program internal default settings.

Lock commands A-115

DONE

INDEX

INDEX

read prompts you for the name of a lock display file which has previously been stored with store. After reading in this file, the lock display window is adjust-ed accordingly.

quit closes the lock display window


<xwhome>/exp/stan/nmr/loc_win/

default - current lock display settings

SEE ALSOlock, edlock

A-116 Lock commands

DONE

INDEX

INDEX

lopo, lopoi

NAMElopo - set the lock parameterslopoi - set the lock parameters interactively

DESCRIPTION

The command lopo reads the lock parameters from edlock table for the sol-vent defined by the acquisition parameter SOLVENT. As such, the lock power, loop gain, loop time, loop filter, lock phase and frequency shift are set to the lock table values of Lpower, LGain, LTime, LFilt, LPhase and Distance, respectively. These values are set on the BSMS unit without performing lock-in.

lopo is useful if you want to observe the lock signal first. The lock-in procedure can then be performed by pressing the Lock On/Off or Autolock key on the BSMS keyboard. Note that

lopo � Autolock is equivalent to lock -acqu

lopo � Lock On/Off is equivalent to lock -noauto

The command lopoi works like lopo, except it does not interpret the param-eter SOLVENT. lopoi shows a list of available solvents from which you can select one. It then sets the lock parameters according to the edlock table.

INPUT PARAMETERSset by the user with eda or by typing solvent etc.:

SOLVENT - sample solventLOCNUC - lock nucleus

set by the user with edlock :

see table 4.1

INPUT FILES




Lock commands A-117

DONE

INDEX

INDEX

probehead - current probehead as defined by edhead


2Hlock - lock table for nucleus 2H19Flock - lock table for nucleus 19F




LOPO

SEE ALSOlock, edlock, lockdisp, lgain, ltime, lfilter

A-119

Chapter 5

Shim commands

This chapter describes the commands which are involved in shimming the magnet. Shimming can be started with reading an appropriate shim set for the current sam-ple and then optimizing the shim from the BSMS keyboard. In automation, the optimization is performed by an automatic shimming procedure. Furthermore, if you are using a gradient probehead, you can perform gradient shimming.

A-120 Shim commands

DONE

INDEX

INDEX

autoshim

NAMEautoshim - autoshim switching

DESCRIPTIONThe command autoshim controls the autoshim function of the BSMS unit. It takes one argument and can be used as follows:

autoshim onturn autoshimming on

autoshim offturn autoshimming off

Entering autoshim on the command line has the same effect as pressing the AUTOSHIM key on the BSMS keyboard. The shims for which the step size is set to a value greater than 0 are optimized. It is typically used in automation.

USAGE IN AU PROGRAMSAUTOSHIM_ON

AUTOSHIM_OFF

SEE ALSOtune, edtune, rsh, wsh, setsh, vish, delsh

Shim commands A-121

DONE

INDEX

INDEX

edtune

NAMEedtune - edit tune file

SYNTAXedtune [<name>]

DESCRIPTION

The command edtune allows you to edit an existing tune file or create a new one. Tune files are used by the tune command that performs automatic shim-ming.

edtune takes one argument and can be used as follows:

edtuneShows a list of existing tune files. You can click an entry to edit the corre-sponding file or you can enter a name in the field Type New Name. In the lat-ter case, an empty file will be opened and can be set up as a new tune file.

edtune <name>Edits the specified tune file. If the specified file does not exist, an error mes-sage will appear.

The format of a tune file is described for the tune command. Two example files, example and example_bsms are delivered with XWIN-NMR.

INPUT FILES<xwhome>/exp/stan/nmr/lists/group/

example - standard tune file for spectrometers with a SCM unitexample_bsms - standard tune file for spectrometers with a BSMS unitmy_tunefile - user defined tune file

SEE ALSOtune, rsh, wsh, setsh, vish, delsh, gradshim

A-122 Shim commands

DONE

INDEX

INDEX

rsh

NAMErsh - read a set of shim values

SYNTAXrsh [<name>]

DESCRIPTION

The command rsh reads a set of shim values to the shim unit. rsh without ar-guments opens a dialog box with a list of available shim sets. When you click on a shim set, its values are loaded to the shim unit. rsh can also be entered with a shim file as an argument.

After reading a shim file, is usually necessary to optimize the shims, especially the Z and Z2 shim. You can do that from the BSMS keyboard or from the BSMS display (command bsmsdisp).

rsh switches the autoshim function of the BSMS unit off. If you press the AU-TOSHIM key on the BSMS keyboard or enter autoshim on, the shims will be continuously optimized during the experiment.

If you specify an argument, then it may contain wildcards; for example:

rsh a* lists all shim files beginning with arsh [m-z]* lists all shim files beginning with m,n,...,z

Shim files can be stored with the command wsh and viewed with vish. Single shims can be set with setsh.

INPUT FILES

<xwhome>/exp/stan/nmr/lists/bsms/

shim files

USAGE IN AU PROGRAMSRSH(name)

Shim commands A-123

DONE

INDEX

INDEX

SEE ALSO

wsh, setsh, vish, delsh, edtune, tune, gradshim

A-124 Shim commands

DONE

INDEX

INDEX

setsh

NAMEsetsh - set a single shim

SYNTAXsetsh [<name>] [<value>]

DESCRIPTION

The command setsh allows you to set single shims. It takes two arguments and can be used in one of the following ways:

setshprompts you for a shim and a value and then sets the specified shim accord-ingly

setsh <shim> prompts you for a value and then sets the specified shim accordingly

setsh <shim> <value> sets the specified shim to the specified value

Entire shim sets can be read to the shim unit with rsh, stored with wsh and viewed with vish.

USAGE IN AU PROGRAMSSETSH(shim, value)

SEE ALSO

rsh, wsh, vish, delsh, edtune, tune, gradshim

Shim commands A-125

DONE

INDEX

INDEX

tune

NAMEtune - perform automatic shimming of the magnet

SYNTAXtune [ <tunefile> | .sx ]

DESCRIPTION

The command tune shims the magnet in an automatic procedure according a shim definition file. This file is called the tune file and can be set up with the command edtune.

The command tune takes one argument and can be used in one of the following ways:

tunedisplays a list of available tune files. When you click an entry, the corresponding tune file is interpreted and auto shimming is performed accordingly.

tune <tunefile>performs auto shimming according to the specified tune file.

tune .sxperforms auto shimming according to the tune file as it is specified for the cur-rent probehead. This tune file can be setup from the edprosol dialog box by clicking File � Edit Tunefile

A example tune file is delivered with XWIN-NMR. You can use this as it is or modify it to your needs and store it under a different name. The statements you can use in a tune file are listed below. Note that some of these statements are set-tings whereas others are commands.

Settings in a tune file:

USE_FIDAREA

Flag indicating to use the area under the FID envelope as a criterion for field homogeneity.

USE_LOCKLEVEL

A-126 Shim commands

DONE

INDEX

INDEX

Flag indicating to use the lock level as a criterion for field homogeneity.

LOCKDWELL n

The number of measurements used for determining the current lock level. The measured values are averaged to suppress the effects of the noise on the lock level. Only used when USE_LOCKLEVEL is defined.

MAXLOCK m

The maximum lock level. Can be used to keep the lock signal from moving out of the display during the shimming procedure.The lock level is displayed at the XWIN-NMR status line while tune is run-ning.

DELAY n

The time (in seconds) between adjusting a shim and reading the new lock lev-el. In the example tune file, DELAY is set to one second which is usually enough for the lock level to settle.

SET <shim> w c

Set the maximum step size (width) and the convergence limit for the SIM-PLEX command. These parameters can be set for each shim separately. An example is:

SET Z1 20 3

TIMES n ..END

Loop structure; all statements within the loop will be executed n times. Nest-ed loops are possible to a depth of five.

Commands in a tune file

ROTATION ON WAIT

Switches the sample rotation on using the spin rate currently set on the BSMS unit.

ROTATION OFF WAIT

Switches the sample rotation off.

Shim commands A-127

DONE

INDEX

INDEX

RSH, RSH <filename>

Reads a shim file. If an argument is specified, RSH will read the correspond-ing shim file. If not, it will read the shim file with the name of the solvent de-fined by the acquisition parameter SOLVENT.

Z s i, Z2 s i, ..., XY s i

Optimizes single shims. These commands take two arguments:

s = step size; the shim increment used as long as the lock level increases i = iterations; the maximum number of steps after passing the maximum

A shim is first changed s units in one direction. If this increases the lock level, the shim is changed again s units in the same direction. This is repeated until a shim change decreases the lock level. Then the direction of change is re-versed and the step size is reduced. This process is continued until one of the following criteria has been met:

• the lock level has not changed significantly during the last step

• the maximum number of iterations (i) has been performed

• the step size has been reduced to one

Examples of shim commands are:

Z 10 3Z2 10 3Z3 10 3

SIMPLEX <shim1 shim2 etc.>

Optimizes the specified shims according to the simplex algorithm which can be used for lock level and FID area shimming. SIMPLEX uses the step size and convergence limit defined by the SET statement (see above). The sim-plex algorithm is described in the example file (see INPUT FILES below).

AUTOSHIM ON <shim1=m, shim2=n, ...>

Switches on the automatic shimming function on the shim unit after the tune command has finished. This command allows you to adjust the shims continuously during the entire experiment. Only the shims that are specified as arguments to the AUTOSHIM ON command will be optimized. For each shim, you can specify the step size used for auto shimming. If you do not specify the step size, the default value of 5 is used. An example of this com-mand is:

A-128 Shim commands

DONE

INDEX

INDEX

AUTOSHIM ON Z1=2 Z2

Since this command becomes effective after the tune command has fin-ished, it can be specified anywhere in the tune file.

AUTOSHIM OFF

Switches off automatic shimming on the shim unit. It makes sure that auto-matic shimming is switched off when it was switched on before, either from the last executed tune file or manually from the BSMS keyboard. Note that it would not make sense to use AUTOSHIM ON and AUTOSHIM OFF within one tune file.

LOCKPHASE s i

Optimize the lock phase. This command takes two arguments:

s = step size i = iterations; the maximum number of steps

As an alternative to the automatic shimming with tune, you can optimize the shims manually from the BSMS keyboard. If the shims are far away from the optimum, you can read a standard shim set with the command rsh and then do manual shimming.

An alternative to the simplex procedure in tune is the AU program simplex.

INPUT FILES<xwhome>/exp/stan/nmr/lists/group/

example - tune file for BSMS (XWIN-NMR 3.1 and newer) 1

example - tune file for SCM/BSN18 (XWIN-NMR 3.0 and older)example_bsms - tune file for BSMS (XWIN-NMR 3.0 and older)

<xwhome>/conf/instr/<instrum>/prosol/<probeID>/

tunefile - tune file for the current probehead (input for tune .sx)

USAGE IN AU PROGRAMSTUNE(tunefile)

1. Note that all Avance spectrometers have BSMS. Some AMX/ARX spectrometers have BSMS, other have SCM/BSN18.

Shim commands A-129

DONE

INDEX

INDEX

TUNESXexecutes the command tune .sx

SEE ALSOedtune, gradshim, rsh, wsh, setsh, vish, delsh

A-130 Shim commands

DONE

INDEX

INDEX

vish

NAMEvish - view a shim file

SYNTAXvish [<name>]

DESCRIPTION

The command vish allows you to view a shim file. It takes one argument and can be used in one of the following ways:

vish opens a dialog box with a list of available shim files. When you click a shim file, it is opened for viewing.

vish. <name>opens the specified shim file for viewing


vish tol* lists all shim files beginning with tolvish [m-z]* lists all shim files beginning with m,n,...,z

Shim files can be stored with wsh and read to the shim unit with rsh. Single shims can be set with setsh.

INPUT FILES

<xwhome>/exp/stan/nmr/lists/bsms/

shim files

SEE ALSOrsh, wsh, setsh, delsh, edtune, tune, gradshim

Shim commands A-131

DONE

INDEX

INDEX

wsh

NAMEwsh - write a set of shim values

SYNTAXwsh [<name>]

DESCRIPTION

The command wsh writes the shim values which are currently installed on the shim unit to a shim file. It takes one argument and can be used in one of the fol-lowing ways:

wshopens a dialog box with a list of currently available shim files. Existing shim files can be overwritten or a new name can be entered.

wsh <name>writes the current shim values to a file with the specified name. The name of a shim file can be freely chosen.


wsh tol* lists all shim files beginning with tolwsh [m-z]* lists all shim files beginning with m,n,...,z

Shim files can be read with the command rsh and viewed with vish. Single shims can be set with setsh.

OUTPUT FILES<xwhome>/exp/stan/nmr/lists/bsms/

shim files

USAGE IN AU PROGRAMSWSH(name)

SEE ALSOrsh, setsh, vish, delsh, edtune, tune, gradshim

A-133

Chapter 6

Probehead commands

This chapter describes the commands which are involved in probehead handling. This involves selecting the current probehead, the tuning and matching procedure and sample insert and eject.

A-134 Probehead commands

DONE

INDEX

INDEX

atma

NAMEatma - automatic tuning and matching of ATM probeheads

USAGEatma [exact | course] [high]

Type atma ? for a complete list of options.

DESCRIPTIONThe command atma performs tuning and matching of an ATM probehead. It will automatically perform the following steps:

1. Stop the sample rotation if it is on.

2. Read the nucleus with the lowest frequency as it was set up with edasp.

3. Determine the optimum sweep width and number of steps.

4. Tune and match the probehead.

5. Repeat step 3 to 4 for all other nuclei which were set up with edasp in the order of increasing frequency.

6. Turn on the sample rotation if it was on before atma was started

The command atma can be used with various options, for example:

atma exact will determine the optimum tuning and matching more pre-cisely then atma without an argument and will therefore be slower.

atma course will determine the optimum tuning and matching less pre-cisely then atma without an argument will therefore be faster.

atma high will start with the nucleus with the highest frequency, and tune and match the probehead for each nucleus in the order of decreasing frequen-cy.

Type atma ? for a complete list of options.

On ATM probeheads, atma can be used instead of the wobb. These two com-mands differ in the following respects:

Probehead commands A-135

DONE

INDEX

INDEX

• atma is fully automatic whereas wobb requires the user to perform the tuning and matching manually.

• atma automatically determines the optimal sweep width and number of steps whereas wobb uses the values of WBSW and WBST, respectively.

• wobb must be terminated with stop or halt whereas atma automati-cally finishes when optimum tuning and matching is reached. If you want to interrupt atma, you can do that with the command kill.

Automatic tuning and matching is not only convenient, it also allows you to tune and match the probehead during automaton. In ICON-NMR, you can choose to do that before each experiment, after each sample change or after each solvent change.

atma is supported with XWIN-NMR 2.6 and later.

For more information on the tuning and matching process, see wobb.

For more information on the command atma and ATM probeheads, see Help � Other topics � Automatic Tuning and Matching.

INPUT PARAMETERSNUC1 - NUC4 - nuclei as defined with edasp

INPUT FILES





<xwhome>/prog/wobble/

acqu_go4 - wobble parameters Pulsprog_X - wobble pulse program

SEE ALSOatmm, wobb


DONE

INDEX

INDEX

atmm

NAMEatmm - manual tuning and matching of ATM probeheads

USAGEatmm [manWbsw]

Type atmm ? for a complete list of options.

DESCRIPTIONThe command atmm is a manual tuning and matching procedure for ATM probeheads. It is not needed very often because ATM probes are designed for au-tomatic tuning and matching with atma. Sometimes, however, the probeheads resonance frequency is so far away from the optimum that atma would take very long to finish or would fail. In practice, this only occurs for certain nuclei at broadband probeheads. In that case, atmm allows you to manually tune and match the probehead for that nucleus.

atmm performs the following steps:

1. It reads the nucleus with the lowest frequency as it was set up with edasp.

2. It determines the optimum sweep width and number of steps.

3. It shows the reflected power (tuning/matching curve) in the XWIN-NMR acquisition data field.

4. It opens the atmm control window from where you can:

• Select the nucleus for which you want to tune and match the probe-head. By default, the nucleus with the lowest frequency is selected.

• Perform course tuning/matching on broadband probeheads. This is the equivalent of setting the sliders on a non ATM probehead to predefined numbers.

• Perform fine tuning/matching while observing the curve in the XWIN-NMR acquisition data field. This is the equivalent of turning the knobs or moving the sliders on a non ATM probehead. See wobb for a description on how to reach the optimum tuning and matching.


DONE

INDEX

INDEX

• Click File � Quit to finish the tuning/matching process.

atmm can be used with various options. For example, atmm manWbsw does not determine the sweep width and number of steps automatically but interprets the parameters WBSW and WBST, respectively. atmm ? will show you a com-plete list of options.

The difference between atmm and wobb is that:

• atmm can only be used on ATM probeheads.

• atmm automatically determines the optimum sweep width and number of steps whereas wobb uses the values of WBSW and WBST, respec-tively.

• atmm allows you to optimize tuning and matching from XWIN-NMR whereas wobb requires you to turn the knobs (or move the sliders) on the probehead.

atmm is supported with XWIN-NMR 2.6 and later.

For more information on the tuning and matching process, see wobb.

For more information on the command atmm and ATM probeheads, see Help � Other topics � Automatic Tuning and Matching.

INPUT PARAMETERSNUC1 - NUC4 - nuclei as defined with edaspWBSW - sweep width (only used by atmm Manwbsw)WBST - number of steps (only used by atmm Manwbsw)

INPUT FILES<du>/data/<user>/nmr/<name>/<expno>/




SEE ALSOatma, wobb


DONE

INDEX

INDEX

edhead

NAMEedhead - edit probehead table

DESCRIPTIONThe command edhead opens the probehead table. Each entry in this table con-tains a probehead name and reference number. A typical entry is:

5 mm Dual 13C/1H [03]

The entry which is defined as the current probehead, is highlighted.

The probehead table has a menu Probe in the upper left corner that offers the fol-lowing commands:

New Probe

The probehead parameter editor will be opened where you can define a new probehead. You can do that by setting the probehead parameters (see below). The name of the new probe will be the combination:

Sample diameter Probe Type Coil Nuclei Part number Serial number

Note that the Part number and Serial Number are only part of newly defined probes, not of the probes in the standard list delivered with XWIN-NMR. The reference number of a new probe will be the first unused number available. This usually the number of the last entry plus one 1.

Copy Probe

The current probehead will be copied to a new probehead with the same name. The new probe is added at the end of the list. The reference number will be the first unused number available. This usually the number of the last entry plus one 1.

Delete Probe

The current probehead will be deleted. Its reference number will be unused until a new probehead is defined.

1. If a probe was deleted and left an unused reference number, this is assigned to the new probe.


DONE

INDEX

INDEX

Define as Current Probe

The highlighted entry will be defined as current probehead. If no entry is highlighted, an error message will appear. If the highlighted probehead has not been defined before, you will be prompted you with the question:

Do you want to create the probe parameterset?

If you click No, no probehead parameters will be stored but the highlighted entry will still be defined as current probehead. If you click Yes, the probe-head parameter editor will be opened (see below).

Edit Probe parameters

When you click this button, a dialog box with various probehead parameters will appear (see below).

Exit

Close the probehead table, saving all changes.

The menu entries Define as current probe, Edit probe parameters and Exit are also available as buttons at the bottom of the edhead dialog box.

The probehead parameter editor displays four groups of parameters:

Production parameters like:

Probe typePart numberSerial number..

Sample parameters like:

Sample diameterSample depth

Temperature parameters like:

Type of sensorLowest allowed temperatureHighest allowed temperature

Coils parameters like:

Number of coils


DONE

INDEX

INDEX

Gas compensationInside coil nucleiOutside coil nuclei

History:

A text field where any information about the probe can be entered

Some probeheads have an additional parameter group, e.g.:

Broadband probes: Tuning and Matching parametersFlow probes: Probe flow parameters

Note the probe parameters are just information for the user. They are not re-quired for the acquisition and they are not interpreted by any XWIN-NMR com-mand.

The current probehead as defined with edhead, is interpreted by the commands edprosol, edlock, lock, lopo and setpre as well as during ICON-NMR automation. At the end of an acquisition the current probehead is stored as the acquisition status parameter PROBHD (see dpa).

edhead can also be executed as a part of the XWIN-NMR configuration suite (command config).


probeheads.all - default probehead list (input of first time edhead)


edhead - Tcl/Tk script that is started by edhead


<xwhome>/exp/stan/nmr/lists/

probeheads - probehead list (input of 2nd and later edhead and output)


probehead - current probeheads name and reference number

<xwhome>/conf/instr/probeheads

<part #>_<serial #>_<reference #>.par - probe parameters


DONE

INDEX

INDEX

SEE ALSO

cf, atma, atmm, wobb


DONE

INDEX

INDEX

ej, ij

NAMEej - eject the sample from the magnetij - insert the sample into the magnet

DESCRIPTION

The command ej ejects the sample from the magnet. It switches on the air flow and keeps it on until it is explicitly switched off, for example with ij.

The command ij inserts the sample into the magnet. This command is used when the magnet air flow is on and the sample is floating on top of it. ij grad-ually reduces the air flow to zero so that the sample is lowered into the magnet.

As an alternative to the command ej and ij, you can also press the LIFT ON/OFF button on the BSMS keyboard.

The SAMPLE DOWN indicator in the shimming panel of the BSMS keyboard is lit when the sample is positioned correctly in the probe. The SAMPLE UP in-dicator is lit when the sample has reached the top of the magnet. The SAMPLE MISSING indicator is lit if the sample is somehow positioned between the mag-net top and the probehead, either moving up or down or being stuck. The latter can happen, for instance, when the air flow is too high.

USAGE IN AUTOMATIONEJIJ

SEE ALSO

ro


DONE

INDEX

INDEX

ro

NAMEro - switch the sample rotation on or off

SYNTAXro [ acqu | off | off wait ]

DESCRIPTION

The command ro switches the sample rotation on or off. It takes two arguments and can be used as follows:

ro allows you to set the spin rate and switch the spinning on. ro first prompts you for the following information:

Spinning on: enter yes to switch the spinning on or no if you only want to set the spin rate.Spinning rate: enter the demand spin rate

ro onSwitches the sample rotation on with the spin rate currently set on the BSMS keyboard (visible when you press the SPIN RATE key).

ro acqu Sets the spin rate to the value of the acquisition parameter RO, then switches rotation on and waits for 60 seconds. If spin rate has not been reached within that time an error message appears.

ro off Switches the sample rotation off.

ro off wait Switches the sample rotation off and waits until the rotation has reached zero. During the waiting time the BSMS unit cannot be accessed by other com-mands.

As an alternative to the command ro, you can press the SPIN ON/OFF, and SPIN RATE keys on the BSMS keyboard or BSMS display (command bsmsdisp)


DONE

INDEX

INDEX

INPUT PARAMETERS

RO - sample rotation frequency (input for ro acqu)




ROTexecutes the command ro acqu.

ROTOFFexecutes the command ro off wait.

SEE ALSOij, ej


DONE

INDEX

INDEX

wobb

NAMEwobb - manual tuning and matching of the probehead

USAGEwobb [high][ext50][raw][f1|f2]

DESCRIPTITION

The command wobb allows you to manually tune and match the probehead. An NMR probehead must be tuned and matched because it is a resonance circuit. If its resonance frequency and impedance are the same as the transmitter frequency and impedance, respectively, the full transmitter power is transferred to the probehead. However, if either or both are different, part of the transmitter power is reflected by the probehead. This results in a longer 90° pulse or, for a given pulse length, a smaller flip angle. Note that a multi nuclear probehead has a res-onance circuit for each nucleus and each nucleus must be tuned and matched separately.

The command wobb is normally used without argument. It can, however, be used with arguments. For example:

wobb highstarts with the nucleus with the highest frequency and continues in the order of decreasing frequency.

wobb ext50uses an external 50 ohm resistor as a reference.

wobb f1starts with frequency channel f1. It continues with the next higher frequency or, if the argument high is also used, with the next lower frequency.

wobb f2starts with frequency channel f2. It continues with the next higher frequency or, if the argument high is also used, with the next lower frequency.

The wobb command allows you to optimize both the probeheads resonance fre-quency (tuning) and impedance (matching). It sends a low power RF signal to the probe and sweeps that signal over a certain frequency range. The number of


DONE

INDEX

INDEX

steps (frequencies) within that range is defined by the acquisition parameter WBST. The width of the frequency range is defined by WBSW. The center fre-quency depends on the nucleus; SFO1 for NUC1, SFO2 for NUC2 etc. The de-viation of the probe impedance from the nominal 50 ohm is shown as function of the frequency in the XWIN-NMR data field. This is the so called wobble curve. At the probeheads resonance frequency, the curve shows a dip, the minimum re-flected power. Tuning the probehead means adjusting its resonance frequency until it reaches SFO1. Matching the probehead means adjusting its impedance until the reflected power reaches zero.

The entire wobble procedure involves the following steps:

1. Stop the sample rotation if this is on, for example with ro off, or by pressing the SPIN ON/OFF button on the BSMS keyboard.

2. Setup the nucleus or nuclei for the current experiment with edasp.This will automatically set the parameters SFO1, SFO2 etc.

3. Click Acquire � Observe fid window or enter acqu to switch to the XWIN-NMR acquisition menu. If, however, tuning and matching is observed on the preamplifier, this step can be skipped. (see below).

4. Enter wobb. The wobble curve will appear in the XWIN-NMR data field showing a dip at a certain frequency. At the center of the data field, you will see a vertical line. If you do not see the dip, it probably lies outside of the data field. In that case, you should click wobb-SW or enter wbchan to increase the sweep width. You can do this while wobb is running.

5. When the dip is visible, you can start tuning and matching as follows:

• turn the tuning knob until the dip lies across the vertical line

• turn the matching knob until the dip has reached a minimum. Match-ing influences tuning, so the dip probably moves away from thecenter.

• turn the tuning knob until the dip lies at the center again. Tuninginfluences matching, so the dip probably moves up again.

• turn the matching knob until the dip reaches a minimum again

• continue this process until the dip lies exactly across the vertical lineand reaches the x-axis.

6. In case of a multi nuclei experiment, you have to switch to the next the


DONE

INDEX

INDEX

nucleus. Note that wobb automatically starts with the nucleus with the lowest basic frequency. You can switch to the nucleus with the next higher frequency in two possible ways:

• press Channel Select at the HPPR. This will automatically select thenucleus with the next higher frequency.

• click wobb-SW or enter wbchan in XWIN-NMR. Answer the ques-tion "Do you want to change the nucleus" with yes.

Repeat step 5 for the current nucleus.

7. If your experiment involves more than two nuclei, repeat step 6 for each further nucleus.

8. Click stop or enter stop on the command line to finish the wobble pro-cedure.

A probehead has a tuning knob (labelled T) and matching knob (labelled M) for each resonance circuit. Most probeheads have two, one for 1H and one for X-nuclei. When the tuning knob reaches the end of its range before the probehead is properly tuned, you should turn it to the middle of its range, adjust matching, then tuning, then matching etc. A similar procedure can be used if the matching knob reaches the end of its range.

The process of tuning and matching can also be followed on the HPPR pream-plifier. Some people find that more convenient and it is necessary when the com-puter screen is not visible from the position of the probehead. The horizontal row of LED’s indicates tuning, the vertical row indicates matching. When you turn the tuning or matching knob at the probehead, you will see how the number of lit LED’s changes. The probehead is perfectly tuned when only one LED (a green one) is lit. The same holds for matching. In practice, proper tuning and matching means that only green LED’s are lit. If the LED update seems to be very slow, this might be caused by the time consuming update of the wobble curve in the XWIN-NMR acquisition display. In that case, you can simply click return to switch to the processing menu (main menu).

Broadband probeheads usually have sliders for tuning and matching rather than turning knobs. These have the advantage that their positions are numbered. The default slider positions for each nucleus are usually written on cards that are kept with the probehead. When wobbling is started with these default values, only some fine tuning and matching is required.

The probehead resonance frequency and impedance is dependent on the sample.


DONE

INDEX

INDEX

This can be a problem in automation, where several samples are measured but the probehead is only matched and tuned on one of them. Bruker ATM probe-heads support automatic tuning and matching which can be preformed on every sample during automation (see description of the commands atmm and atma).

INPUT PARAMETERSset by the user with eda or by typing wbst, wbsw etc.:

WBST - number of wobble stepsWBSW - wobble sweep width

set by the user with edasp or eda � NUCLEI:

NUC1 - NUC4 - the nuclei for which the probehead is tuned and matchedSFO1 - SFO4 - irradiation frequency





SEE ALSO

atma, atmm, edasp

A-149

Chapter 7

Parameter handling commands

This chapter describes commands which are involved in parameter handling. This involves the setting of acquisition parameters, probehead/solvent dependent parameters and nuclei assignment. Furthermore, the usage of predefined parame-ters sets is discussed.

A-150 Parameter handling commands

DONE

INDEX

INDEX

ased, as

NAMEased - edit the acquisition parameters used in the current pulse programas - same as ased but prompts the user for each parameter

DESCRIPTION

The command ased opens a dialog box in which you can set the acquisition pa-rameters which are used for the current experiment. This means that ased shows much less parameters then eda which shows all acquisition parameters.

ased shows three types of parameters, namely parameters that are:

• used in all experiments like NS, TD etc.

• defined by edasp like NUC1, SFO1, NUC2, SFO2 etc.

• interpreted by the current pulse program, e.g. D[1], P[1], PL[1] etc.

ased compiles and interprets the pulse program defined by PULPROG. For pulses, delays and constants, the parameter description in the right column of the ased window is taken from the comment section at the end of the pulse pro-gram.

as works like ased except that it prompts the user for each parameter.


for all experiments:

PULPROG - pulse program used for the acquisitionTD - time domain; number of raw data pointsNS - number of scansDS - number of dummy scansSWH - spectral width in HzAQ - acquisition time in seconds RG - receiver gainDW - dwell timeDE - pre-scan delay

for each frequency channel defined with edasp:

NUCx - nucleus for channel x

Parameter handling commands A-151

DONE

INDEX

INDEX

SFOx - irradiation frequency for channel x

all delays, pulse lengths, power levels etc. defined in the pulse program, e.g.:

D[1] - relaxation delayP[1] - 90° pulse lengthPL[1] - power level for pulsePCPD[1] - CPD pulse length

INPUT FILES

<xwhome>/exp/stan/nmr/lists/pp/

the pulse program defined by PULPROG



OUTPUT FILES<du>/data/<user>/nmr/<name>/<expno>/


SEE ALSO

eda, edcpul


DONE

INDEX

INDEX

dpa

NAMEdpa - display the acquisition status parameters

DESCRIPTIONThe command dpa displays the acquisition status parameters. These are set by acquisition commands and represent the status of the raw data.

The dpa dialog box offers the following buttons/fields:

• Donecloses the dpa window or, on 2D or 3D data, go to the next dimension

• 1-Col changes to one column display mode. In this mode a short description is shown for each parameter.

• Parameter allows you to search for a parameter. Just enter the parameters name (or a part of it) and hit the Enter key. The dpa window will scroll to the parameters position. If nothing happens, the parameter does not exist or is on the currently displayed page.

• Nextselects the next parameter which starts with the string in the Parameter field

Acquisition status parameters can also be viewed by entering their names on the command line. For example:

On a 1D dataset:

1s ns displays the acquisition status parameter NS

On a 2D dataset:

2s td displays the F2 acquisition status parameter TD

1s tddisplays the F1 acquisition status parameter TD


DONE

INDEX

INDEX

On a 3D dataset, the preposition 3s can be used for the F3 dimension.

The NMR Superuser can change the dpa dialog box, for example remove pa-rameters which are not used. This can be done from the Windows Explorer or from a UNIX shell by editing the file normdp (see below).

INPUT FILES<xwhome>/exp/stan/nmr/form/acqu.l/

normdp - format file for dpa

On 2D and 3D data the directories acqu2.l and acqu3.l contain a normdp file for the indirect dimensions.

<du>/data/<user>/<name>/nmr/<expno>/


On 2D and 3D data the files acqu2s and acqu3s are used for the indirect di-mensions, respectively (see also chapter 2.3).

SEE ALSO

eda, lpa, dp, dpc, dpo, dpp, dpg, dpgx


DONE

INDEX

INDEX

eda

NAMEeda - edit acquisition parameters

DESCRIPTIONThe command eda opens a dialog box in which you can set all acquisition pa-rameters. This dialog box offers the following buttons/fields:

• Savesaves all parameters

• 1-Col changes to one column display mode. In this mode a short description is shown for each parameter.

• Parameter allows you to search for a parameter. Just enter the parameters name (or a part of it) and hit the Enter key. The eda window will scroll to param-eters position and select it. Note that the parameter might be on the cur-rent page.

• Nextselects the next parameter which starts with the string in the Parameter field.

• Cancel leaves eda without saving any changes

The disadvantage of eda is that it shows many parameters, most of which do not have to be changed for a standard experiment. Generally, it is more convenient to use ased to set the acquisition parameters. This command only shows the pa-rameters which are actually used for the current experiment.

Apart from using eda or ased, you can also set acquisition parameters by en-tering there names on the command line, e.g.:

ns prompts you to enter the number of scans.ns 1000sets the number of scans to 1000

For 2D datasets, eda shows one column of parameters for the F2 dimension and


DONE

INDEX

INDEX

one for the F1 dimension The 1-Col button is not available. Note that most pa-rameters are not dimension specific and, as such, appear for the F2 dimension only. 2D parameters can also be set from the command line, e.g.:

td 4ksets the F2 time domain to 4k

2 td 4ksets the F2 time domain to 4k (same as td 4k)

1 td 4ksets the F1 time domain to 4k

For 3D dataset, eda shows an extra column for the third dimension.

The NMR Superuser can change the eda dialog box, for example remove pa-rameter which are not used. This can be done from the Windows Explorer or from a UNIX shell by editing the file acqu.e (see below).

INPUT AND OUTPUT PARAMETERSAll acquisition parameters.

INPUT FILES<xwhome>/exp/stan/nmr/form/

acqu.e - format file for eda

INPUT AND OUTPUT FILES<du>/data/<user>/<name>/nmr/<expno>/

acqu - acquisition parameters for the acquisition (direct) dimensionacqu2 - acquisition parameters for F1 indirect dimension (2D) or F2 (3D)acqu3 - acquisition parameters for the F1 dimension (3D)

SEE ALSOased, dpa


DONE

INDEX

INDEX

edasp

NAMEedasp - set up nuclei and spectrometer routing

DESCRIPTIONThe command edasp allows you to set up the nuclei and the spectrometer rout-ing for the current experiment. It opens the routing table showing the current nu-clei selection and amplifier routing. Here you can specify the nucleus or nuclei to be used for the experiment. For the f1 logical frequency channel, you can click the NUC1 button and select a nucleus from the appearing list. The basic frequen-cy, BF1, is automatically set. Then you can specify the frequency offset; OFSH1 for 1H or OFSX1 for X nuclei. The irradiation frequency SFO1 is automatically calculated as the sum of the basic frequency and frequency offset. Note that the parameters NUC1, BF1 and SFO1 also appear in eda but cannot be set from there. However, the frequency offset (OFSH1 or OFSX1) appears in eda as O1 and can be set from there. In a multi nuclear experiment, you can set up the pa-rameters for channel f2, f3 etc. in the same way as described for f1.

The routing table also shows the spectrometer routing. The hardware elements which have been detected when the spectrometer was configured (with cf or config) will appear in this list. When you select a nucleus for a certain chan-nel, the default routing is automatically set. Normally, this can be left as it is. Only in very special cases it is useful to change it. The routing table consists of the following stages:

Channel---FCU---Amplifier---Swibox/I ---Swibox/O---Preamplifier

You can set up the routing by connecting an element from one stage to an ele-ment of the next stage. A connection can be installed or removed by clicking the two elements involved. The routing must follow following rules:

a) Between the logical frequency channels and FCU’s any combination is allowed but only one to one.

b) An FCU can be connected to one amplifier only but an amplifier can be connected to multiple FCU’s. Furthermore, FCU1 can only be connected to the first three amplifiers and FCU2 can only be connected to the first four amplifiers.


DONE

INDEX

INDEX

c) The first four Amplifiers are automatically connected to Switchbox input in a fixed way. These connections cannot be changed.

d) Between the Switchbox input and Switchbox output, any connection is allowed but only one to one.

e) Between the Switchbox output and the Preamplifier modules, any con-nection is allowed but only one to one. Make sure that the cables are con-nected accordingly.

f) The output of the fifth and sixth amplifier must be connected directly to the Preamplifier modules. Any combination is allowed but only one to one and only to Preamplifier modules which are not connected to a Switchbox output.

Avance spectrometers which are used for solid state experiments usually contain high power amplifiers with two output stages:

• a low power output: typically 150 W for 1H or 300 W for X nuclei.

• a high power output: typically 1000 W for 1H or X nuclei

The second output appears as an extra stage in the routing table to the right of the switchbox. If you use the second output stage, the switchbox is always by-passed.

If you make a routing connection which is not allowed, you will get a message that it is illegal. You must remove it before you can save the routing table. Some connections are allowed but not recommended. In that case, you only get a warn-ing.

Two extra switches are available to control the routing:



When you change these settings, you must click the DEFAULT button to make them effective.

At the bottom of the NUCLEI table you will find the following buttons:

SAVE - save the routing table and quit

SWITCH F1/F2 - exchange the F1 and F2 nucleus including the frequency


DONE

INDEX

INDEX

and frequency offset

SWITCH F1/F3 - exchange the F1 and F3 nucleus including the frequency and frequency offset

DEFAULT - set the default amplifier routing for the current nuclei

CANCEL - quit without saving any changes

PARAM - shows the routing parameters

In a 2D dataset, NUCLEI has a different functions in the two dimensions. In F2, it works like in 1D experiments; it opens the routing table. In F1, it opens the nuclei list and allows you to select the nucleus for this dimension. The same principle holds for 3D data; in F3, NUCLEI opens the routing table, in F2 and F1 it opens the nuclei list.

The spectrometer routing is stored under the current dataset in the acquisition parameters FCUCHAN, RSEL, SWIBOX, PRECHAN and HPMOD (see the description of these parameters). These can be viewed by clicking the PARAM button in the routing table. Note that these parameters appear in eda and can be set from there. This, however is not very common as setting them from the rout-ing table is much more convenient. In Bruker parameter sets (see rpar), the routing parameters have been set according to the configured hardware. This corresponds to the routing that will be set by clicking the default button in the routing table.

However, you only need to set the following switches:



and click SAVE to store them.

The Preferred preamplifier determines the default preamplifier module (selec-tive or unselective) for X-nuclei. The Preferred output for 19F determines the default output of the switchbox (X or 19F) for 19F.

In XWIN-NMR 3.1 and newer, the connections between the Switchbox output and the Preamplifier modules are fixed; they cannot be changed. However, if you start edasp with the argument setpreamp, you can change these connections or remove them all by clicking CLEAR ALL. If you make any changes here, you


DONE

INDEX

INDEX

must make sure that the cables at the spectrometer are connected accordingly. Note that, in XWIN-NMR 3.1 and newer, the command edasp setpreamp is implicitly called as a part of spectrometer configuration (command cf).


set from edasp by setting Preferred preamplifier:

DEFRSEL - preferred preamplifier (default routing)

set from edasp by setting Preferred output for 19F:

DEF19F - preferred output for 19F (default routing)

set graphically from edasp by connecting routing elements:

FCUCHAN - logical frequency channel - FCU connectionsRSEL - FCU - amplifier connectionsSWIBOX - Switchbox input - Switchbox output connectionsPRECHAN - Switchbox output - Preamplifier module connectionsHPMOD - high power amplifier - Preamplifier module connections

INPUT AND OUTPUT FILES<du>/data/<user>/<name>/nmr/<expno>/


<xwhome>/conf/instr/<INSTRUM>/

specpar - routing parameters

SEE ALSOedsp, eda, cf, config, expinstall


DONE

INDEX

INDEX

getprosol

NAMEgetprosol - get probehead and solvent dependent parameters

DESCRIPTIONThe command getprosol reads the probehead and solvent dependent param-eters (the prosol parameters) and copies them to the corresponding acquisition parameters. The relations between the prosol and acquisition parameters are shown in table 7.1. These are the default relations which apply to most standard high resolution experiments. Protein, DNA/RNA and LC-NMR experiments re-quire different relations which are defined in the files, triple, triple_na and lcnmr, respectively (see INPUT FILES). To use relations other then de-fault, the so called relations file must be specified in the pulse program. You can do that by editing the pulse program (with edpul or edcpul) and adding the line:

/* relations <filename> */

before the actual pulse sequence. Note that the /* */ characters are obligatory! To look at an example, you can enter edpul lc2 or edpul zgesgp. Note that the file default, for default relations can, but does not need to be specified in the pulse program.

getprosol replaces the command gpro and the AU program pulsesort which were used in XWIN-NMR versions older than 3.0.


DONE

INDEX

INDEX

Description edprosol eda

F1 90° hard pulse length P90[F1] P[0], P[1]

F1 180° hard pulse length P90[F1]*2 P[2]

F2 90 ° hard pulse length P90[F2] P[3]


F1 Tocsy spin lock 60° pulse length PTOC[F1]*0.66 P[5]

F1 Tocsy spin lock 90° pulse length PTOC[F1] P[6]

F1 Tocsy spin lock 180° pulse length PTOC[F1]*2 P[7]

F1 Roesy spin lock pulse length PROE[F1] P[15]

Gradient 1 pulse length P_grad1 P[16]

F1 Tocsy trim pulse length P_mlev P[17]

Gradient 2 pulse length P_grad2 P[19]

F3 90° hard pulse length P90[F3] P[21]


F1 HSQC trim pulse length P_hsqc P[28]

F2 Roesy spin lock pulse length PROE[F2] P[31]

F1 90° hard pulse power level PL90[F1] PL[1]



F1 Tocsy spin lock power level PLTOC[F1] PL[10]

F1 Roesy spin lock power level PLROE[F1] PL[11]

F2 CPD power level PLCPDP[F2] PL[12]

F2 Second CPD (bilev) power level PLCPD2[F2] PL[13]

F3 CPD power level PLCPDP[F3] PL[16]

F2 Homodecoupling power level PLHD[F2] PL[24]

Gradient recovery delay D_grad D[16]

F2 CPD pulse length PCPDP[F2] PCPD[2]

F2 CPD pulse length PCPDP[F3] PCPD[3]

Table 7.1 Default relations between prosol and acquisition parameters


DONE

INDEX

INDEX


see table 7.1

INPUT FILES<xwhome>/conf/instr/<instrum>/prosol/relations

default - relations file for most experimentstriple - relations file for Protein experimentstriple_na - relations file for DNA experimentslcnmr - relations file for LC-NMR

<xwhome>/conf/instr/<instrum>/prosol/<probeID>/<solvent>

nucleus.channel.amplifier - prosol parameters


acqu - acquisition parametersrelations - copy of the input relations file

SEE ALSOedprosol, eda


DONE

INDEX

INDEX

rpar

NAME rpar - read a parameter set

SYNTAXrpar [<name> [<type>]]

DESCRIPTION

The command rpar reads a parameter set to the current dataset. It takes two ar-guments and can be used as follows:

• rparshows a list of existing parameter sets. When you click on a parameter set, you will get a list of parameter types available in that set. You can select one or more parameter types and then click Copy to copy them to the current dataset. Alternatively, you can click Copy All to copy all parameter types.

• rpar <name>shows a list of parameter types available in the parameter set <name>. You can select one or more parameter types and then click Copy to copy them to the current dataset. Alternatively, you can click Copy All to copy all parameter types.

• rpar <name> <type>copies the parameter type <type> of the parameter set <name>

The Cancel button in there rpar dialog box allows you to quit without read-ing any parameters.

The following parameter types exist:

• acqu - acquisition parameters

• proc - processing parameters

• plot - graphics and plot parameters

• outd - output device parameters

• title - plot title (user defined parameter sets only)

• level - 2D or 3D contour levels (user defined parameter sets only)


DONE

INDEX

INDEX

• all - all of the above parameter types

rpar only reads those parameter types which are selected and which exist in the specified parameter set.

Bruker parameter sets are delivered with XWIN-NMR and installed with the com-mand expinstall. They all contain the parameter types acqu, proc, plot and outd.

User defined parameter sets can be created with wpar and contain the parameter types that were selected during creation. These include the types acqu, proc, plot, outd, title and, for 2D or 3D data, level.

rpar allows you to read parameters sets of various dimensionalities: 1D, 2D, etc. If the dimensionality of the current dataset and the parameter set you want to read are the same, e.g. both 1D, the dataset parameter files are overwritten. If the current dataset contains data (raw and/or processed data), these are kept. Fur-thermore, the status parameters are kept so you still have a consistent dataset. However, as soon as you process the data, the new processing parameters are used, the processed data files are overwritten and the processing status parame-ters are updated. When you start an acquisition, the new acquisition parameters are used, the raw data are overwritten and the acquisition status parameters are updated. If the current dataset is 1D, contains data (raw and/or processed) and you read a 2D parameter set, rpar will warn you that the current data will be deleted and ask you whether or not you want to continue. However, this warning will not appear if you enter the command with two arguments, i.e.:

rpar <name> <type>

In that case, data files of a different dimensionality are simply deleted. The rea-son is that is that rpar with two arguments is used in automation.

After reading a parameter set with rpar, you can modify parameters of the var-ious types with the commands:

• eda - acquisition parameters

• edp - processing parameters

• edg and edgx - plot parameters

• edo - output device parameters

• edlev - contour levels

• setti - plot title


DONE

INDEX

INDEX

The first argument of rpar may contain wildcards, for example:

rpar C* shows all parameter sets beginning with the letter Crpar [H-Z]* shows all parameter sets beginning with a letter between H and Z.

INPUT FILES<xwhome>/exp/stan/nmr/par/<1D parameter set>/

acqu - acquisition parameters (parameter type acqu)proc - processing parameters (parameter type proc)meta - plot parameters (parameter type plot)meta.ext - extended plot parameters (parameter type plot)outd - output device parameters (parameter type outd)title - plot title (parameter type title)

<xwhome>/exp/stan/nmr/par/<2D parameter set>/

acqu - F2 acquisition parameters (parameter type acqu)acqu2- F1 acquisition parameters (parameter type acqu)proc - F2 processing parameters (parameter type proc)proc2 - F1 processing parameters (parameter type proc)meta - plot parameters (parameter type plot)meta.ext - extended plot parameters (parameter type plot)outd - output device parameters (parameter type outd)title - plot title (parameter type title)level - 2D contour levels (parameter type level)

3D parameter sets also contain the files acqu3 and proc3 for the third dimen-sion but do not contain the file meta.ext. User defined parameter sets may also contain the files title (1D and 2D) and level (2D and 3D).

OUTPUT FILES

<du>/data/<user>/nmr/<1D data name>/<expno>/

acqu - acquisition parameters (parameter type acqu)

<du>/data/<user>/nmr/<1D data name>/<expno>/pdata/<procno>/

proc - processing parameters (parameter type proc)meta - plot parameters (parameter type plot)meta.ext - extended plot parameters (parameter type plot)


DONE

INDEX

INDEX

outd - output device parameters (parameter type outd)title - plot title (parameter type title)


acqu - F2 acquisition parameters (parameter type acqu)acqu2 - F1 acquisition parameters (parameter type acqu)


proc - F2 processing parameters (parameter type proc)proc2 - F1 processing parameters (parameter type proc)meta - plot parameters (parameter type plot)meta.ext - extended plot parameters (parameter type plot)outd - output device parameters (parameter type outd)title - plot title (parameter type title)level - 2D contour levels (parameter type level)

3D data also contain the files acqu3 and proc3 for the third dimension but do not contain the file meta.ext.


RPAR(name, type)

SEE ALSOwpar, dirpar, delpar, renpar, expinstall


DONE

INDEX

INDEX

wpar

NAMEwpar - write a parameter set

SYNTAXwpar [<name> [< type>]]

DESCRIPTION

The command wpar stores the parameters of the current dataset in a parameter set. This parameter set is then available for general usage and can be read to any dataset with rpar.

wpar allows you to overwrite an existing parameter set or to enter a new name. It takes two arguments an can be used in one of the following ways:

wpar opens a dialog box with a list of existing parameter sets. You can click one of them, or enter a name in the field Type New Name. A new dialog box will then open showing a list parameter types. If you chose an existing parameter set, the existing parameter types in it are highlighted. You can select/deselect parameter types by clicking their entries. Then you can click Copy to store the highlighted types. Alternatively, you can click Copy All to store all types.

wpar <name>shows a list of parameter types. If you specified an existing parameter set, the existing parameter types in it are highlighted. You can select/deselect param-eter types by clicking their entries. You can then click Copy to store the high-lighted types. Alternatively, you can click Copy All to store all types.

wpar <name> <type>stores parameters of type <type> to parameter set <name>. If <type> already exists in <name>, it is overwritten.

The Cancel button in the wpar dialog box allows you to quit without storing any parameters

The following parameter types exist:

• acqu - acquisition parameters


DONE

INDEX

INDEX

• proc - processing parameters

• plot - graphics and plot parameters

• outd - output device parameters

• title - plot title

• level - 2D or 3D contour levels

• all - all of the above parameter types

wpar is often used as part of the following sequence:

1. Define a new dataset with edc or new.

2. Enter rpar to read a Bruker parameter set which defines the experiment you want to do.

3. Modify the acquisition parameters (with eda) to your preference and run the acquisition.

4. Modify processing parameters (with edp) to your preference and proc-ess the data.

5. Modify the plot parameters (with edg) to your preference, set the output

device parameters (with edo) and plot the dataset 1.

6. Store the parameters with wpar for general usage.

The first argument of wpar may contain wildcards, for example:

wpar C* lists all parameter sets which begin with the letter Cwpar [H-Z]* lists all parameter sets which begin with a letter between H and Z.

INPUT FILES


acqu - acquisition parameters (parameter type acqu)


proc - processing parameters (parameter type proc)meta - plot parameters (parameter type plot)meta.ext - extended plot parameters (parameter type plot)outd - output device parameters (parameter type outd)

1. Alternatively, you can use XWIN-PLOT whose layout is not part of the parameter set.


DONE

INDEX

INDEX


acqu - F2 acquisition parameters (parameter type acqu)acqu2 - F1 acquisition parameters (parameter type acqu)


proc - F2 processing parameters (parameter type proc)proc2 - F1 processing parameters (parameter type proc)meta - plot parameters (parameter type plot)meta.ext - extended plot parameters (parameter type plot)outd - output device parameters (parameter type outd)

3D data also contain the files acqu3 and proc3 for the third dimension but do not contain the file meta.ext. Note that only the files whose parameter type has been selected within wpar are input files.

OUTPUT FILES


acqu - acquisition parameters (parameter type acqu)proc - processing parameter (parameter type proc)meta - plot parameters (parameter type plot)meta.ext - extended plot parameters (parameter type plot)outd - output device parameters (parameter type outd)title - plot title (parameter type title)


acqu - F2 acquisition parameters (parameter type acqu)acqu2- F1 acquisition parameters (parameter type acqu)proc - F2 processing parameters (parameter type proc)proc2 - F1 processing parameters (parameter type proc)meta - plot parameters (parameter type plot)meta.ext - extended plot parameters (parameter type plot)outd - output device parameters (parameter type outd)title - plot title (parameter type title)level - 2D contour levels (parameter type level)

3D parameter sets also contain the files acqu3 and proc3 for the third dimen-sion but do not contain the file meta.ext and title. Note that only the files whose parameter type has been selected within wpar are output files.


DONE

INDEX

INDEX


WPAR(name, type)

SEE ALSOrpar, dirpar, delpar, renpar, expinstall

A-171

Chapter 8

Pulse and AU program commands

This chapter describes commands for the setup of pulse programs, gradient pro-grams, CPP programs and AU programs. Furthermore, it describes the setup of various lists which can be used in acquisition like variable pulse or variable delay lists.

A-172 Pulse and AU program commands

DONE

INDEX

INDEX

edau

NAMEedau - create or edit AU programs

SYNTAXedau [<name>]

DESCRIPTION

The command edau allows you to list, create or edit AU programs. When used without argument, a two column list appears with the Bruker AU programs on the right side and the user defined AU programs on the left side. When you click a Bruker AU program, it is shown in view mode which means it cannot be mod-ified. When you click a user defined AU program, it is opened with an editor and can be modified. When you close the view window or editor, you are prompted for one of the following options:

(c)ompile - compile the AU program(b)ack - go back to displaying the list of AU programs(q)uit - quit without compiling the AU program

When you choose c for compilation (the default option), the AU program will be compiled using a C compiler. After successful compilation, the AU program can be executed by typing its name.

When edau is entered with an argument, the specified AU program will be opened. This allows you to write a new AU program or modify an existing one. The argument may contain wildcards, e.g. edau a* displays a list of all AU pro-grams starting with a.

Bruker AU programs must be installed once with expinstall before they can be opened with edau. The installation must be repeated when a new version of XWIN-NMR is installed. By default, Bruker AU programs are opened in view mode, which means they cannot be modified. However, if you enter edau and click the Edit button, the NMR Superuser password is requested and the pro-gram switches to Edit mode. When you now click a Bruker AU program, it will be opened with an editor and can be modified. Nevertheless, we recommend to leave the Bruker AU programs unchanged. If you want a modified version, just create a new AU program, read in the Bruker AU program, modify it to your

Pulse and AU program commands A-173

DONE

INDEX

INDEX

needs and store it.

edau uses the editor which is defined in the XWIN-NMR User Interface. If you want to use a different editor, type setres and modify the entry Editor.

For details on writing, compiling, and executing AU programs please refer to the AU reference manual (click Help � Other topics � Writing AU programs).

INPUT FILES<xwhome>/exp/stan/nmr/au/src/

AU program source files

If the AU program is compiled (c option of edau):

/<xwhome>/exp/stan/nmr/au/

makeau - AU compilation scriptvorspann - C language definition filesubmacro - preprocessor replacing macros and includes

<xwhome>/prog/include/

aucmd.h - AU macro definition file

/<xwhome>/prog/include/inc

AU program includes

OUTPUT FILES<xwhome>/exp/stan/nmr/au/src/

AU program source files

If the AU program is compiled (c option of edau):


AU program executable binary files

SEE ALSO

expinstall, comepileall, cpluser, cplbruk, delau, renau


DONE

INDEX

INDEX

edcgp

NAMEedcgp - edit current gradient program

SYNTAXedcgp [<name>]

DESCRIPTION

The command edcgp allows you to create or edit the current gradient program. The current gradient program is defined as the gradient program of the fore-ground dataset as defined by the acquisition parameter GRDPROG.

edcgp takes one argument and can be used as follows:

• edcgpopen the current gradient program

• edcgp <name> open the gradient program <name> and make it the current gradient pro-gram.


edcgp SIN* lists all gradient programs beginning with SINedcgp [m-z]* lists all gradient programs beginning with m,n,...,z

INPUT PARAMETERSto be set with eda or by typing grdprog :

GRDPROG - the current gradient program (input of edcgp)

OUTPUT PARAMETERScan be viewed with eda or by typing grdprog :

GRDPROG - the current gradient program (output of edcgp <name>)

INPUT FILES

<xwhome>/exp/stan/nmr/lists/gp/*


DONE

INDEX

INDEX

gradient programs



OUTPUT FILES



SEE ALSOedgp


DONE

INDEX

INDEX

edcpd

NAMEedcpd - edit composite pulse decoupling (CPD) programs

SYNTAXedcpd [<name>]

DESCRIPTION

The command edcpd allows you to list, create or edit CPD programs. If you enter edcpd without arguments, a list of all CPD programs is displayed. The list includes both the Bruker and the user defined CPD programs. When you click on a CPD program, it is opened with an editor. Alternatively, or you can enter a name in the field "Type New Name" to create a new CPD program. The Print button allows you to print the list of CPD programs.

If you enter the command with an argument, e.g. edcpd <name>, the CPD pro-gram <name> is opened or, if it does not exist, it is created. The argument may contain wildcards; e.g. edcpd a* displays a list of all CPD programs which start with a.

Bruker CPD programs must be installed with expinstall before they can be opened with edcpd.

edcpd uses the editor which is defined in the XWIN-NMR User Interface. You can change it by typing setres and specify it in the field Editor.

INPUT AND OUTPUT FILES<xwhome>/exp/stan/nmr/lists/cpd/*

Bruker and user defined CPD programs

SEE ALSOexpinstall


DONE

INDEX

INDEX

edcpul

NAMEedcpul - edit the current pulse program

SYNTAXedcpul [<name>]

DESCRIPTION

The command edcpul allows you to create or edit the current pulse program. The current pulse program is defined as the pulse program of the foreground da-taset as defined by the acquisition parameter PULPROG.

edcpul takes one argument and can be used as follows:

• edcpulopens the current pulse program

• edcpul <name> opens the pulse program <name> and makes it the current pulse pro-gram.

Bruker pulse programs are opened in view mode which means they cannot be modified. User defined pulse programs are opened with an editor and can be modified.


edcpul cos* lists all pulse programs beginning with cosedcpul [m-z]* lists all pulse programs beginning with m,n,...,z

INPUT PARAMETERSto be set with eda or by typing pulprog :

PULPROG - the current pulse program (input of edcpul)

OUTPUT PARAMETERScan be viewed with eda or by typing pulprog :

PULPROG - the current pulse program (output of edcpul <name>)


DONE

INDEX

INDEX

INPUT FILES

<xwhome>/exp/stan/nmr/lists/pp

Bruker and user defined pulse programs




acqu - acquisition parameters (output of edcpul <name>)

SEE ALSO

edpul, edcpd, edgp


DONE

INDEX

INDEX

edgp

NAMEedgp - edit gradient programs

SYNTAXedgp [<name>]

DESCRIPTION

The command edgp allows you to list, create or edit gradient programs. If you enter edgp without arguments, a list of all gradient programs is displayed. This list includes both the Bruker and the user defined gradient programs. When you click a gradient program it will be opened with an editor. Alternatively, you can enter a name in the field "Type New Name" to create a new gradient program. The Print button allows you to print the list of gradient programs.

If you enter the command with an argument, i.e. edgp <name>, the gradient program <name> is opened or, if it does not exist, it is created. The argument may contain wildcards, e.g. edgp a* displays a list of all gradient programs which start with a.

Bruker gradient programs must be installed with expinstall before they can be opened with edgp.

edgp uses the editor which is defined in the XWIN-NMR User Interface. You can change it by typing setres and specify it in the field Editor.

INPUT AND OUTPUT FILES<xwhome>/exp/stan/nmr/lists/gp/*

gradient programs

SEE ALSOedcpul, edpul, edcgp, expinstall


DONE

INDEX

INDEX

edlist

NAMEedlist - edit various lists

SYNTAXedlist [<type> [<name>]]

DESCRIPTION

The command edlist allows you to list, create or edit various lists like delay lists, pulse lists and frequency lists. Most of these lists are used during acquisi-tion. edlist can be used in one of the following ways:

edlist - displays all lists typesedist <type> - displays all entries of the list type <type>edlist <type> <name> - creates/edits the list <name> of type <type>

The second argument may contain wildcards, e.g. edlist vd a* displays all variable delay lists which start with a.

A variable delay list can be set up and used as follows:

• create a variable delay list with edlist

• set the acquisition parameter VDLIST to the name of that list

• specify the vd statement in the pulse program

Other lists can be used in a similar way. At the end of this description we will discuss an alternative way to use lists, circumventing the acquisition parameter.

All lists that can be used by during acquisition are displayed in table 8.1. They typically contains one value per line and the number of lines is unlimited. The type of the list that is interpreted is determined by the type of pulse program statement. The list name is determined by an acquisition parameter.

Delay lists

Delay lists contain any number of delay values with the corresponding units, e.g.:

10m2s


DONE

INDEX

INDEX

where m = milliseconds and s = seconds. They are interpreted by the pulse program statements:

vd - read value from the current position in the delay listivd - increment the delay list position to the next valuevdidx - set the index to position n in the delay list

Pulse lists

Pulse lists contain any number of pulse length values with the corresponding units, e.g.:

10µ20m

where µ = microseconds and m = milliseconds. They are interpreted by the pulse program statements:

list type descriptiondefined by

parameterread by pulse

progr. statements

vd delay list VDLIST vd, ivd, vdidx

vp pulse list VPLIST vp, ivp, vpidx

f1frequency list

(Avance)FQ1LIST, FQ2LIST

etc.fql, fq2, fq3 etc.

f1, f2, f3frequency list

(A*X)F1LIST, F2LIST etc. o1, o2, o3

vc counter list VCLIST lo to x times c, ivc

va amplitude list VALIST define list<power>

ds dataset list DSLISTwr #n, wr ##, ifp, dfp, rfp

vt temperature list VTLISTRVTLIST, VT,

IVTLIST, DVTLISTa

masr MAS spin rate list AU prog multimas

wave Shaped pulse list SP07 sp1, sp2 etc.

Table 8.1 Lists used in acquisition

a. Note that these are AU program macros rather than pulse program statements


DONE

INDEX

INDEX

vp - read value from the current position in the pulse listivp - increment the pulse list position to the next valuevpidx - set the index to position n in the pulse list

A variable pulse list can only be used for hard pulses, not for shaped pulses.

Frequency lists

Frequency lists contain the irradiation frequency preceded by the letter O on the first line (optional) and any number of frequency offset values on subse-quent lines, e.g.:

O 500.13300031503200

They are interpreted by pulse program statements like:

30µ fq1:f1read the current value from the list defined by FQ1LIST to channel f1

d1 fq2:f1 read the current value from the list defined by FQ2LIST to channel f1

d11 fq3:f2 read the current value from the list defined by FQ3LIST to channel f2

Note that the fq1, fq2 etc. statements must be specified with a delay. In con-trast to the vd and vp statements, they automatically increment the current position in the list to the next value.

In the above example, the offset values in the list are added to the frequency specified on the first line, independent of the channel. If, however, the first line would be omitted, the offset values in the list are added to the values of SFO1, SFO2 etc. for the respective channels.

Counter lists

A variable counter list contains any number of loop counter values, e.g.:

4720

They are interpreted by the pulse program statement:


DONE

INDEX

INDEX

lo to x times c where x is a pulse program label and c is the value at the current position of the counter list

ivc increment the counter list position to the next value

Variable amplitude (power) lists

A variable amplitude list contains any number of power values, e.g.:

-6.00.03.06.0

The entries represent attenuation values in dB.

The usage of a VA list is different from pulse and delays lists. You must de-fine the statement by which a VA list is accessed in the pulse program. Such a statement can have any name, for example the name vanam is used in the examples below. The suffixes .inc, .dex and .res can be used to incre-ment, decrement and reset the lists position, respectively. Furthermore, the caret operator (^) allows you to read a list value and increment the list posi-tion with one statement. The following pulse program entries illustrate the use of a variable amplitude list:

define list<power> vanam = <$VALIST>definition of the power list

d1 vanam:f2 vanam.dec set the power to the current value of the list and decrement the index

d1 vanam[2]:f3set the power to the second value of the list

"vanam.idx = vanam.idx + 3" increment the list index by 3

d1 vanam^:f4set power to the current value of the list increment the index

As an alternative to using a list defined by the parameter VALIST, you can explicitly define a variable amplitude (power) list filename or even the list values in the pulse program. The following examples illustrates such defini-


DONE

INDEX

INDEX

tions:

define list<power> vanam=<my_filename>define list<power> vanam={10 30 50 70}

Note that the second definition does not require a list file.

Note that variable amplitude lists can only be accessed using define state-ments as described above. The statement va does not exist. More information on using variable amplitude lists can be found under:


Dataset lists

A dataset list contains any number of dataset definition, e.g.:

sucrose 1 1 C:\ guest newsucrose 2 1 C:\ guest newfructose 1 1 D:\ guest old

where the option new/old is used to delete/keep a possibly existing dataset.

They are interpreted by the pulse program statements:

wr #n write the data to the dataset defined at the position n of the dataset list

wr ## write the data to the dataset defined at the current position of the dataset list

ifpincrement the position in the dataset list

dfpincrement the position in the dataset list

rfpreset the position in the dataset list to the first entry

Temperature lists

A variable temperature list contains any number of temperature values (in Kelvin), e.g.:

300


DONE

INDEX

INDEX

320340

Temperature lists are interpreted by the AU program macros:

RVTLISTopen the temperature list defined by VTLIST

VTread value from the current position in the temperature list and set the tem-perature unit accordingly

IVTLISTincrement the current position in the temperature list to the next value

DVTLISTdecrement the current position in the temperature list to the previous value

Note that temperature lists are only interpreted by AU program macros, not by pulse program statements.

Shaped pulse lists

A shaped pulse list is a JCAMP files that defines a shaped pulse. It contains a JCAMP header and a list of relative power values (X) and phase values (Y). An example of a shaped pulse list is:

##TITLE= /u/exp/stan/nmr/lists/wave/Crp60comp.4##JCAMP-DX= 5.00 Bruker JCAMP library##DATA TYPE= Shape Data##ORIGIN= Bruker Analytik GmbH##OWNER= <demo>##DATE= 99/02/09##TIME= 19:06:33##MINX= 0.000000e+00##MAXX= 1.000000e+02##MINY= 1.110700e-01##MAXY= 3.599617e+02##$SHAPE_EXMODE= Adiabatic##$SHAPE_TOTROT= 1.800000e+02##$SHAPE_BWFAC= 0.000000e+00##$SHAPE_INTEGFAC= 1.564030e-01##$SHAPE_MODE= 0


DONE

INDEX

INDEX

##NPOINTS= 4000##XYPOINTS= (XY..XY)0.000000e+00, 1.833010e+027.893400e-01, 1.779120e+021.578620e+00, 1.725340e+022.367810e+00, 1.671660e+023.156850e+00, 1.618090e+023.945700e+00, 1.564630e+024.734300e+00, 1.511280e+025.522600e+00, 1.458040e+026.310560e+00, 1.404900e+027.098130e+00, 1.351870e+027.885250e+00, 1.298950e+028.671890e+00, 1.246140e+029.457980e+00, 1.193440e+02....

Shaped pulse lists are interpreted by a pulse program statement like:

p13:sp2:f1

which executes a shaped pulse with length P13 on channel f1, using the pulse defined by second entry (sp2) in the table defined by the acquisition param-eter SP07.

Masr lists

MASR lists contain any number of MAS spin rate values, e.g.:

3000350040004500

They are interpreted by the AU program multimas. This AU program will ask you if you want to use a list or enter the start and increment value inter-actively. if you choose the former (default), it will offer you the available MASR lists.

There are alternative ways of defining and using lists in acquisition. Rather than using a predefined statements like vd, you can define your own statement in the pulse program to access a certain list. For example, the statements:


DONE

INDEX

INDEX

define list<delay> vdnam = <$VDLIST>define list<delay> vdfil = <my_file>define list<delay> vdval = {0.1 0.2 0.3 0.4}

allows you to use the statements vdnam, vdfil and vdval to read a value from a delay list. The use of lists via define statements is fully described above for the variable amplitude lists. More information on user defined lists can be found un-der:


The edlist command also shows various files which are programs rather than lists of values, for example pulse programs, CPD programs, gradient programs and macros. These, however, are normally opened with the dedicated commands edpul, edcpd, edgp and edmac rather than with edlist.


<xwhome>/exp/stan/nmr/lists

pp - pulse programscpd - CPD programsgp - gradient programswave - shaped pulse listspreemp - preemphasis listsds - variable dataset listsva - variable amplitude (power) listsvc - variable counter listsvd - variable delay listsvp - variable pulse lists vt - variable temperature listsf1 - variable frequency listsf2, f3 - variable frequency lists (A*X spectrometers only)mac - XWIN-NMR macrosroi - 2D integral rangesscl - scaling region filesmasr - MAS spin rate list

SEE ALSO

edmisc, edpul, edcpd, edgp, edmac


DONE

INDEX

INDEX

edpul

NAMEedpul - edit a pulse program

SYNTAXedpul [<name>]

DESCRIPTION

The command edpul allows you to list, edit or create pulse programs.

edpul without arguments opens a dialog box with two columns of pulse pro-grams. The right column shows the Bruker pulse programs, the left column the user defined pulse programs. When you click a Bruker pulse program, it is opened in view mode which means it cannot be changed. When you click a user defined pulse program, it is opened with an editor and can be modified. Instead of opening an existing pulse program, you can enter a name in the field "Type New Name" to create a new one.

The edpul dialog box also contains a button Edit which allows you to switch to Edit-mode and modify Bruker pulse programs. Be careful: they are overwrit-ten when you install a new version of XWIN-NMR. Therefore, if you want to mod-ify a Bruker pulse program you should store it under a new name.

edpul <name> opens the pulse program <name>. If <name> does not exist, an empty file is created and opened with an editor.


edpul cos* lists all pulse programs beginning with cosedpul [m-z]* lists all pulse programs beginning with m,n,...,z

Bruker pulse programs must be installed with expinstall before they can be opened with edpul.

edpul uses the editor which is defined in the XWIN-NMR User Interface. If you want to use a different editor, type setres and modify the entry Editor.

INPUT FILES

<xwhome>/exp/stan/nmr/lists/pp/*


DONE

INDEX

INDEX

Bruker and user defined pulse programs

OUTPUT FILES<xwhome>/exp/stan/nmr/lists/pp/*

user defined pulse programs

SEE ALSO

edcpul, edcpd, edgp, edcgp, expinstall, edlist

A-191

Chapter 9

Acquisition commands

This chapter describes all commands involved in data acquisition. This includes parameter optimization, the actual data acquisition and stopping a running experi-ment. Most experiments which involve a single acquisition are started with the command zg and run until they are finished. Other experiments involve multiple acquisitions executed with an AU program or with ICON-NMR.

A-192 Acquisition commands

DONE

INDEX

INDEX

acqu

NAMEacqu - switch to the acquisition menu

DESCRIPTIONThe command acqu switches XWIN-NMR to the acquisition menu. This is the menu where the raw data (FID) is displayed. Typing acqu is equivalent to click-ing Acquire � Observe fid window. This command can only be applied from the processing menu (main menu).

In principle, an acquisition can be started from the main menu simply by typing zg or�running an acquisition AU program like au_zg. Furthermore, all acqui-sition commands are available under the Acquire menu item. Nevertheless, there are several reasons to switch to the acquisition menu first:

• to tune and match the probe by optimizing the wobble curve in the acqui-sition data field (command wobb)

• to adjust acquisition parameters interactively by observing the effect on a single scan FID (command gs)

• to observe the accumulation of the FID during acquisition (command zg)

If a long term acquisition has been started and is no longer observed, it is recom-mended to switch back to the processing menu by clicking return.

SEE ALSO

wobb, rga, gs, zg

Acquisition commands A-193

DONE

INDEX

INDEX

butselnmr

NAMEbutselnmr - easy acquisition interface for selective experiments

DESCRIPTIONThe command butselnmr opens an icon box from which you can run 1D se-lective NMR experiments. It is and easy to use interface that is especially meant for the novice or occasional users.

The icon box contains buttons for the following actions:

1. Create New DatasetAllows you to define a new dataset and switches the display to that dataset (executes the XWIN-NMR command edc).

2. LockAllows you to select the solvent and then performs the auto lock-in (exe-cutes the XWIN-NMR command lock).

3. Tune/Match ProbeSwitches to the acquisition menu and allows you to tune and match the probehead (executes the XWIN-NMR command wobb).

4. Automatic ShimmingPerforms shimming according to the tune file defined for the current probe-

head 1 (executes the XWIN-NMR command tune .sx).

5. routine PROTON/def. regions Runs a 1D proton experiment performing the following steps:

• prompts the user for the experiment number (EXPNO)

• executes the XWIN-NMR command rpar PROTON all to read the PROTON parameter set

• executes the XWIN-NMR command getprosol to read the probe and solvent dependent parameters

• shows the experiment time and allows the user to actually start the acqui-sition (by clicking OK) or stop (by clicking Cancel). In the latter case,

1. A probehead dependent tune file can be defined from the edprosol dialog box.


DONE

INDEX

INDEX

the dataset has been created and the acquisition can be started at a later time, for example with xaua.

• selects the region for selective excitation and stores it as reg file.

selective pulse calib.this button allows you to determine the 90° selective pulse

selective excitation, sel.ext. with gradients etc. these buttons allow you to perform selective experiments

User defined #1, User defined #2these button allow you to perform user defined eperiments.It executes the AU program User_au_1 that must be setup by the user.

6. Processing Processes multiple FIDs that are stored in a series of contiguous experi-ments numbers (EXPNO’s). It prompts you for the first EXPNO and the number of EXPNO’s and then performs the command efp (em, ft, pk) on each EXPNO. Note that butselnmr actually runs the AU program mul-tiefp to perform this task.

7. Plot Plots the current data by executing the XWIN-NMR command plot.

8. ContinueIf the acquisition hangs for some reason, clicking this button continues with the next experiment.

9. Exit Exits the butselnmr window

For each button a help text is available that appears when you move the cursor over the buttons.

INPUT FOLDERS

<xwhome>/exp/stan/nmr/par/

PROTON/* - routine proton experiment


butselau - butselnmr AU program binary executablebutsel90 - AU program to determine the 90° selective pulse (executable)multiefp - AU program to process a series of 1D data (executable)


DONE

INDEX

INDEX


butselau - butselnmr AU program sourcebutsel90 - AU program to determine the 90° selective pulse (source)multiefp - AU program to process a series of 1D data (source)


butselnmr - Tcl/Tk script that is started by butselnmr

SEE ALSO

buttonnmr


DONE

INDEX

INDEX

buttonnmr

NAMEbuttonnmr - easy acquisition interface for common experiments

DESCRIPTIONThe command buttonnmr opens an icon box from which you can run com-mon 1D and 2D NMR experiments. It is and easy to use interface that is espe-cially meant for the novice or occasional users.

At the top of the window, the field Xnucleus allows you to select the X-nucleus you want to measure. This feature exists for XWIN-NMR 3.1 and newer. For ear-lier versions, X-nuclei measurements are restricted to 13C.

The icon box offers you buttons for the following actions:

1. Create New DatasetAllows you to define a new dataset and switches the display to that dataset (executes the XWIN-NMR command edc).

2. LockAllows you to select the solvent and then performs the auto lock-in (exe-cutes the XWIN-NMR command lock).

3. Tune/Match ProbeSwitches to the acquisition menu and allows you to tune and match the probehead (executes the XWIN-NMR command wobb).

4. Automatic ShimmingPerforms shimming according to the tune file defined for the current probe

head 1 (executes the XWIN-NMR command tune .sx).

5. routine PROTON Runs a 1D proton experiment performing the following steps:

• prompts the user for the experiment number (EXPNO)

• executes the XWIN-NMR command rpar PROTON all to read the PROTON parameter set

1. A probehead dependent tune file can be defined from the edprosol dialog box.


DONE

INDEX

INDEX

• executes the XWIN-NMR command getprosol to read the probe and solvent dependent parameters

• shows the experiment time and allows the user to actually start the acqui-sition (by clicking OK) or stop (by clicking Cancel). In the latter case, the dataset has been created and the acquisition can be started at a later time, for example with xaua.

6. X nucleus without 1Hdec., X nucleus 1Hdec. with NOE, ect.these buttons allow you to perform the Bruker standard experiments that corresponds to the button name and the X-nucleus defined at the top of the window (XWIN-NMR 3.1 and newer).

routine 13C, DEPT90 13C, ect.these buttons allow you to perform the 13C experiment that corresponds to the button name (XWIN-NMR 3.0 and older).

7. User defined #1these button allow you to perform a user defined experiment. It executes the AU program User_au_1. You can create this AU program with the com-mand edau User_au_1. In the same way, you can activate the button User defined #2.

8. Processing Processes the raw data. For a 1D experiment, this involves the command sequence ef, apk and abs, for a 2D experiment the command xfb (for more information on these commands see the Processing Reference Man-ual).

9. Plot Plots the data by executing the XWIN-NMR command plot.

10.ContinueIf the acquisition hangs for some reason, clicking this button continues with the next experiment.

11.Exit Exits the buttonnmr window

For each button a help text is available that appears when you move the cursor over the buttons.

INPUT FOLDERS

<xwhome>/exp/stan/nmr/par/


DONE

INDEX

INDEX

PROTON/* - routine proton experimentC13CPD/* - routine 13C experimentC13DEPT90/* - DEPT90 13C experimentC13DEPT135/* - DEPT135 13C experimentCOSY90SW/* - COSY experimentNOESYPHSW/* - NOESY experimentMLEVPHSW/* - COSY experimentCOSYGPSW/* - gradient COSY experimentINVBPHSW/* - HMQC experimentINV4LPLRNDSW/* - HMBC experimentINVIETGPSW/* - gradient HMQC experimentINV4GPLPLRNDSW/* - gradient HMBC experiment


buttonau - buttonnmr AU program (binary)


buttonau - buttonnmr AU program (source)


buttonnmr - Tcl/Tk script that is started by buttonnmr

SEE ALSO

butselnmr


DONE

INDEX

INDEX

expt

NAMEexpt - display the experiment time

DESCRIPTIONThe command expt calculates and displays the experiment time for the current data set. If this exceeds the time you have available, you can reduce the number of scans (parameter NS) until the experiment time is acceptable.

For 2D and 3D experiments, expt also compares the file size of the raw data with the available disk space.

INPUT PARAMETERSNS - number of scansAQ - acquisition time in seconds

SEE ALSO

zg, gs


DONE

INDEX

INDEX

go

NAMEgo - perform an acquisition and add to existing data

DESCRIPTIONThe command go starts an acquisition on the current dataset adding to possibly existing raw data. It works like zg, except that it does not overwrite existing da-ta. If raw data already exist, go will add the new data to them. This is, for exam-ple, useful if the signal to noise of your spectrum is too low and you want to acquire additional scans. If no data exist, go has the same results as zg.

If you have stopped an acquisition with halt or stop you can, in principle, continue it with go. Note, however, that the acquisition might have been stopped in the middle of a phase cycle and go starts a new phase cycle. Therefore, if you want to be able to stop and continue an acquisition, we recommend to use the commands suspend and resume (see the description of these commands).

In XWIN-NMR 3.0 and older, the go command can only be used on 1D data. In XWIN-NMR 3.1 and newer, it can also be used in 2D and 3D experiments. Note that if you enter halt or stop during a 2D or 3D acquisition it might stop in the middle of a second or third dimension increment (see above). However, this problem only occurs when you use the wr statement to write the data to disk. In XWIN-NMR 3.1 and newer, you can use the mc statement instead. In that case, the go command continues a 2D or 3D acquisition at the position where it was stopped. Caution: if you increment or decrement any pulses, delays or phases within the acquisition loop, you must do that within one of the mc arguments F1PH, F1QF etc., for example:

d1 mc #1 to 1 F1PH(id0, ip1)

Most acquisitions are started with zg and run until they have finished. As such, the command go is not used very often. It is, however, used in some Bruker AU programs like noediff, noemult, deptcyc and multicyc.

Note the difference between the XWIN-NMR command go and the pulse program statement go (See pulse programming manual).


DONE

INDEX

INDEX


see zg

INPUT AND OUTPUT FILESsee zg

USAGE IN AU PROGRAMSGO

SEE ALSO

zg, suspend, resume


DONE

INDEX

INDEX

gs

NAMEgs - go setup; interactive parameter optimization during acquisition

DESCRIPTITIONThe command gs allows you adjust parameters interactively during an acquisi-tion. The FID display is continuously updated showing the effect of each param-eter change.

gs repeatedly executes the current pulse program but only up to the first go=n or rcyc=n statement. Therefore, gs:

• does not accumulate data

• does not interpret the phase list

• does not write data to disk

In order to see the effect of the parameter changes on the FID, you must first go to the acquisition menu. You can do that by clicking Acquire � Observe fid win-dow or by entering acqu on the command line. The command gs will open a dialog box with a set of acquisition parameters. If you do not see the dialog box, it is probably iconified and you must first click its icon.

The dialog box only shows the parameters which are typically set during gs like irradiation frequencies, pulse lengths and power levels. By default, the irradia-tion frequency offset is selected for adjustment. A slider is available for each nu-cleus which has been set with edasp. You can adjust the frequency offset O1 by putting the cursor on its slider, pressing the left mouse button and moving the mouse. Alternatively, you can increase/decrease the value by clicking or press-ing to the left/right of the slider. Other parameters can be changed in the same way. The following parameters can be changed from the gs dialog box:

SFO1 - SFO8 - irradiation frequency for channel f1- f8O1 - O8 - irradiation frequency offset for channel f1- f8PL[0-31] - power levelsSP[0-31] - shape power AMP[0-31] - amplitude (XWIN-NMR 3.1 and newer)PHCOR[0-31] - reference phasesRG - receiver gain


DONE

INDEX

INDEX

P[0-31] - pulse lengthsD[0-31] - delays

Note that moving the RG slider causes an exponential change in the receiver gain. Therefore, it is often necessary to decrease the sensitivity before changing RG. The effect of changing RG will be shown immediately in the FID display. For all other parameters in the above list, the effect of a change will be shown after one or two scans.

The GS dialog box also contains the following buttons:

• sens*10 - increase the sensitivity of the sliders by a factor of ten

• sens/10 -- decrease the sensitivity of the sliders by a factor of ten

• save - save the parameter that was changed last

• save all - save all changes

• reset - reset the parameter that was changed last

• reset all - reset all changes

• stop acquisition - stop the acquisition and leave the gs dialog box

As an alternative to moving sliders, you can also change parameters from the XWIN-NMR command line while gs is running. If you change a parameter from the above list, the slider value will be automatically updated and the effect will be shown in the FID display. For all other parameters, the effect of a change will not be shown. The entered value is, however, stored and becomes effective when a new acquisition command is executed (for example with gs, zg or rga).

INPUT AND OUTPUT PARAMETERSSee the parameter list above.

INPUT AND OUTPUT FILES<du>/data/<user>/nmr/<name>/<expno>/


SEE ALSOzg, go, rga


DONE

INDEX

INDEX

halt

NAMEhalt - halt the acquisition after of the current scan

DESCRIPTIONThe command halt stops the acquisition after the current scan and writes the data to disk. It is the regular command to stop a running acquisition. Note that halt does not complete the current phase cycle.

If, for some reason, a running or hanging acquisition cannot be stopped with halt, you can try the stop command. If that does not work either, you can use kill. This command will show all active processes and you can click the go module to stop the acquisition

OUTPUT PARAMETERS

all acquisition parameters

OUTPUT FILESIn a 1D dataset:


fid - raw dataacqus - acquisition parameters

In a 2D dataset:


ser - raw data acqus - F2 acquisition status parameters acqu2s - F1 acquisition status parameters

In a 3D dataset:


ser - raw dataacqus - F3 acquisition status parametersacqu2s - F2 acquisition status parameters


DONE

INDEX

INDEX

acqu3s - F1 acquisition status parameters

SEE ALSOstop, zg, go, rga, wobb


DONE

INDEX

INDEX

iconnmr

NAMEiconnmr - user interface for routine spectroscopy and automation

DESCRIPTITIONThe command iconnmr starts the an icon driven user interface ICON-NMR for routine spectroscopy and automation. ICON-NMR can also be started from the desktop. It is fully described the ICON-NMR manual. The online version of this manual can opened by clicking Help from the ICON-NMR window.


DONE

INDEX

INDEX

ii

NAMEii - initialize interface

DESCRIPTIONThe command ii initializes the spectrometer interface. It tries to access all hardware parts of the spectrometer which are needed for the current experiment and loads the acquisition parameters.

ii must be executed once when the spectrometer has been switched off.

INPUT PARAMETERS

all acquisition parameters

USAGE IN AU PROGRAMSII

SEE ALSOzg


DONE

INDEX

INDEX

popt

NAMEpopt - parameter optimization

DESCRIPTIONThe command popt allows you to optimize acquisition parameters like pulses and delays. Before you start an optimization, you must run one acquisition with acquisition parameters as they are (not optimized) and process the data. On the resulting spectrum, you must define the spectral range (a peak or group of peaks) to be used for optimization. You can do that by clicking the left mouse button in the data field to put the cursor on the spectrum and then click the middle mouse button on both side of the desired region. The XWIN-NMR display will automat-ically be adjusted to show the selected region only. You must now store this re-gion by entered dpl1 and answer each question by hitting the Enter key.

The popt dialog box allows you to create an entry for each parameter you want to optimize. By default, it shows only one entry; more parameters can be added by clicking the button Add parameter. Furthermore the following fields are offered:

On/Off Only parameters which are switched On will be optimized

Parameterthe parameter to be optimized. If a parameter is not checked, it will be stored as comment in the optimization protocol.

OPTIMUMthe optimization criterion (see below)

STARTVAL the first value of the parameter

ENDVAL the last value of the parameter (empty for INC ≠ 0 and VARMOD = LIN)

NEXPnumber of experiments (empty for INC ≠ 0 and VARMOD = LIN)

VARMOD


DONE

INDEX

INDEX

parameter variation mode: linear or logarithmic

INCparameter increment value

The optimization criterion OPTIMUM can take the following values:

POSMAX - the maximum value of a positive peakNEGMAX - the maximum value of a negative peakMAGMAX - the maximum magnitude value of a peakMAGMIN - the minimum magnitude value of a peakINTMAX - the maximum value of an integralINTMIN - the minimum value of an integralZERO - zero intensity of a peak

At the bottom of the dialog box you will find the following buttons:

Start optimize : start the optimization for all checked parameters

Halt optimize : stop the optimization

Read protocol : open a text file with the optimization result

Add parameter : add a parameter entry

Read parameter file : read an external popt setup file(e.g. from another dataset)

SAVE - save the current optimization setup

RESTORE - restore the last saved optimization setup

Update data set - update popt setup after changing to a different dataset

EXIT - exit the popt dialog box

Clicking the button Start optimize will start the optimization process. Note that it runs on the current dataset. For each parameter, a series of acquisitions will be performed. The result of this is a series of spectra (actually spectral regions) that are displayed in one screen and show the optimum parameter value. They are stored as one processed data file under the current dataset name and experiment number but under a different processing number. For the first parameter that is optimized this is PROCNO 999, for the second parameter PROCNO 998 etc. As such, you must start popt on a dataset with PROCNO < 900. The result will also be stored in the so called protocol file (see OUTPUT PARAMETERS)

At the top of the dialog box you will find the following check buttons:


DONE

INDEX

INDEX

Store as 2D data (ser file)If checked, the result of the optimization (a series of 1D spectra) will be stored as a 2D dataset in EXPNO 899. However, if the source dataset PROC-NO is greater than 100, the EXPNO of the destination 2D data will bePROCNO - 100.

Run optimization in backgroundIf checked, the foreground dataset will remain the same during the optimiza-tion. If it is not checked, the XWIN-NMR display will change to PROCNO 999 where the optimization result is displayed.

The AU program specified in AUNM will be executedIf checked, the AU program defined by AUNM will be executed instead of the command zg.

If you want to rerun an optimization, you must first return to the starting PROC-NO.

The command popt replaces the AU programs paropt, paroptlin, paroptlog and parray, which were used in XWIN-NMR versions older than 3.0.


acqu - acquisition parameterspopt.array - parameter optimization setup (input of RESTORE)popt.protocol - parameter optimization result (input of Read protocol)

<du>/data/<user>/nmr/<name>/<expno>/pdata/<procno>/

proc - processing parameters


popt - Tcl/Tk script that is started by popt


poptau - AU program that runs the optimization (executable)popthalt - AU program that halts the current optimization (executable)


poptau - AU program that runs the optimization (source)


DONE

INDEX

INDEX

popthalt - AU program that halts the current optimization (source)

OUTPUT FILES<du>/data/<user>/nmr/<name>/<expno>/pdata/999

1r - processed data containing the optimization result of the first parameter

<du>/data/<user>/nmr/<name>/<expno>/pdata/998

1r - processed data containing the optimization result of the 2nd parameter


popt.array - parameter optimization setup (output of SAVE)popt.protocol - parameter optimization result (output of Start optimize)

<du>/data/<user>/nmr/<name>/899/

ser - 2D raw data containing the optimization result

SEE ALSOgs


DONE

INDEX

INDEX

resume

NAMEresume - resume a suspended acquisition

DESCRIPTITIONThe command resume resumes an acquisition that has been suspended.

An acquisition can be suspended with the command suspend. When this is en-tered the acquisition holds as soon as the pulse program statement suspend or calcsuspend is encountered. If the pulse program does not contain such a statement, suspend has no effect. Alternatively, an acquisition can be suspend-ed with the pulse program statement autosuspend or calcautosuspend. They automatically hold the acquisition, without user interaction. The command resume continues acquisition that was suspended, either automatically or with the command suspend.

For more information on the suspend pulse program statements click:


A resumed acquisition does not start with dummy scans. This can be a problem if the recycle delay is shorter then 4 times the T1 value of the measured nucleus.

Note that the suspend information is temporarily stored on the spectrometer FCU, not on disk. As soon as you enter stop or halt, or switch of the spec-trometer, the suspend information is lost and the acquisition cannot be resumed.

SEE ALSO

suspend, zg, go


DONE

INDEX

INDEX

rga

NAMErga - automatic receiver gain optimization

DESCRIPTIONThe command rga automatically optimizes the receiver gain. It performs an ac-quisition with varying receiver gain and finally sets this just below the value where no overflow occurs. In fact, rga repeatedly executes the current pulse program but only up to the first go=n or rcyc=n statement.

If you already know the proper value for the receiver gain, you can simply set RG in eda or by typing rg on the command line.

OUTPUT PARAMETERScan be viewed with eda or by typing rg :

RG - receiver gain

USAGE IN AUTOMATIONRGA

SEE ALSOgs, zg, go


DONE

INDEX

INDEX

stop

NAMEstop - stop the acquisition immediately

DESCRIPTIONThe command stop stops the acquisition immediately without writing the data to disk. Note that in most 1D experiments, the data are only written at the end of the acquisition and using stop would cause a complete loss of data. As such, it is used in case of emergency. Further, it can be used to stop the command gs. To stop a normal acquisition the halt command is used.

Instead of entering stop on the command line, you can also click the stop but-ton.

If, for some reason, a running or hanging acquisition cannot be stopped with halt or stop, you can use kill. This command will show all active process-es and you can click the go module to stop the acquisition

SEE ALSO

halt, zg, go, rga, wobb


DONE

INDEX

INDEX

suspend

NAMEsuspend - suspend a running acquisition

DESCRIPTITIONThe command suspend allows you to hold a running acquisition. When it is entered, the acquisition holds as soon as the pulse program statement suspend or calcsuspend is encountered. If the pulse program does not contains such a statement, suspend has no effect. Alternatively, an acquisition can be suspend-ed with the pulse program statement autosuspend or calcautosuspend. They automatically hold the acquisition, without user interaction. The command resume continues acquisition that was suspended, either automatically or with the command suspend.

Note that the suspend information is temporarily stored on the spectrometer FCU, not on disk. As soon as you enter stop or halt, or switch of the spec-trometer, this information is lost and the acquisition cannot be resumed.

Standard Bruker pulse programs do not contain any suspend statements. There-fore, suspend can only be used with user defined pulse programs which con-tain a suspend statement at a certain position.

SEE ALSOresume, zg, go


DONE

INDEX

INDEX

tr

NAMEtr - transfer data to disk during the acquisition

DESCRIPTITIONThe command tr transfers (writes) data to disk during a 1D acquisition. This is, for example, useful if you want to do a Fourier transform and view the spectrum before the acquisition has finished. Another reason to use tr is to save the cur-rently acquired scans of a long term acquisition. This avoids losing all data in case of a power loss.


fid - 1D raw dataacqus - acquisition status parameters

SEE ALSOzg, go


DONE

INDEX

INDEX

xau, xaua, xaup

NAMExau - execute an AU programxaua - execute the AU program specified with AUNMxaup - execute the AU program specified with AUNMP

SYNTAXxau [<name>]xaua xaup

DESCRIPTIONThe command xau allows you to execute an AU program. It is not used very often because AU programs are normally executed simply by entering their names. The command xau is needed in the following cases:

• the AU program has not been compiled yet

• an XWIN-NMR command with the same name exists

• to call an Au program from an AU program (using the macro XAU)

Note that usually AU programs have already been compiled with edau, com-pileall, cplbruk or cpluser. Furthermore, it is not recommended to give an AU program the same name as an XWIN-NMR command. Before you start writing a new AU program, just type in the name you want to give it to find out if this name is already in use.

AU programs can be executed in three different ways:

xau a list of all AU programs appears, you can click one to execute it

xau <name> compiles the AU program <name> (if it is not compiled yet) and executes it

<name> executes the AU program <name> (if it is compiled)

Furthermore, you can use the commands xaua and xaup to execute AU pro-grams. These commands take no argument but execute the AU program which


DONE

INDEX

INDEX

is specified by the parameters AUNM and AUNMP, respectively. In all Bruker parameter sets, these parameters are set to relevant Bruker AU programs. For ex-ample, in the parameter set PROTON, AUNM = au_zg and AUNMP = proc_1d. When parameter sets are used in automation (ICON-NMR), the AU programs specified by AUNM and AUNMP perform the acquisition and the processing, respectively.

AU programs run in background and several of them can run simultaneously. You can use the command follow to see which AU programs and which part within each AU program are currently running. The command kill can be used to stop a running (or hanging) AU program.

For details on writing, compiling, and executing AU programs please refer to the XWIN-NMR AU reference manual (click Help � Other topics � Writing AU programs).

INPUT PARAMETERS set by the user with eda or by typing aunm :

AUNM - acquisition AU program name for xaua

set by the user with edp or by typing aunmp :

AUNMP - processing AU program name for xaup

INPUT FILES<xwhome>/exp/stan/nmr/au/src/

AU program source files (only input if the AU program is not compiled yet)


AU program binary executables

<du>/data/<user>/<name>/nmr/<expno>/

acqu - acquisition parameters (input file for xaua)

<du>/data/<user>/<name>/nmr/<expno>/pdata/<procno>/

proc - processing parameters (input file for xaup)

USAGE IN AU PROGRAMSXAU(name)


DONE

INDEX

INDEX

XAUA

XAUP

XAUPWXAUPW waits until the AU program has finished before the next statement is executed whereas XAUP doesn’t. XAUA works like XAUPW is this re-spect.

SEE ALSO

edau, delau, renau, expinstall, compileall, cplbruk, cpluser


DONE

INDEX

INDEX

zg

NAMEzg - zero go: perform an acquisition

DESCRIPTIONThe command zg performs an acquisition on the current dataset, overwriting possibly existing data. This involves the following sequence of actions:

1. Read the acquisition parameters

2. Compile the pulse program defined by the acquisition parameter PUL-PROG

3. Execute the pulse program. For most pulse programs this involves:

• the acquisition of DS dummy scans

• the acquisition of NS real scans, accumulating the data

• storing the accumulated data to disk

4. Update the acquisition status parameters

Before you can start an acquisition with zg, you will normally have to prepare the experiment. This typically involves the following command sequence:

edhead - define the current probehead

edprosol - define the probehead and solvent dependent parameters

edc or new - define a new dataset and make it the current dataset

wobb or atma - tune and match the probehead (atma only for ATM probes)

lockdisp - open the lock display window

lock - lock the magnetic field

rsh or gradshim - read shim values or use gradient shimming

rpar - read a standard parameter set for the experiment you want to do

getprosol - get the probehead and solvent dependent parameters

edasp - set up nuclei (NUC1, NUC2 etc.) and the spectrometer routing

ased or eda- adjust the acquisition parameters to your needs


DONE

INDEX

INDEX

zg - acquire the data

They type of experiment is mainly determined by the pulse program. A simple 1D Bruker pulse program is zg, which contains the following lines:

1 ze ;zero memory, reset scan counter and phase lists, enable dummy scans, label 1

2 d1 ;relaxation delay with length D1, label 2 p1 ph1 ;pulse with length P1 and phase ph1 go=2 ph31 ;sample TD points with phase ph31, loop to 2

; times NS+DS wr #0 ;write the data to the current dataset exit ;end of the pulse program

ph1=0 2 2 0 1 3 3 1 ;phase program (list) used for the RF pulseph31=0 2 2 0 1 3 3 1 ;phase program (list) used for the receiver

The RF pulse p1 is executed on the default channel (f1) with the default power level (PL1). The loop to label 2 will be performed NS times to accumulate this number of scans. The wr statement lies outside of this loop which means the data are only written to disk once, at the end of the experiment.

After zg has been started, you can observe the running acquisition in the acqui-sition menu. You can go there by clicking Acquire � Observe fid window or by entering acqu on the command line. Here the FID is displayed and continuously updated. Furthermore, an information window will appear showing the current scan, the total number of scans and the residual experiment time. You can go to the acquisition menu before or after you enter the command zg.

The purpose of dummy scans is to reach steady state conditions concerning T1 relaxation. This is necessary whenever the recycle delay of the experiment is shorter then 4 times the T1 value of the measured nucleus. Furthermore, dummy scans can be used to establish a stable temperature. This is especially important in decoupling experiments where the irradiation high power increases the sam-ple temperature. The number of dummy scans is determined by the acquisition parameter DS. In the pulse program, the ze statement explicitly enables the go statement to perform dummy scans. The zd statement disables the execution of dummy scans.

In most 1D experiments, the acquired data are written to disk only once, at the end of the experiment. You can, however, use the command tr to write data to disk while the acquisition is running. This is, for example, useful if you want to


DONE

INDEX

INDEX

do a Fourier transform and view the spectrum after a few scans. Another reason to use tr is to save the currently acquired scans of a long term experiment. This avoids losing all data in case of a power loss. In multidimensional experiments, the wr statement is part of a loop, and as such, is executed for each increment in the indirect dimension(s). Note that in XWIN-NMR 3.0 or later, Bruker 2D and 3D pulse program do not contain a wr statement. It has been replaced by the mc statement which performs both the disk write and loop back function.

zg allows you to perform 1D or multi dimensional acquisition. The dimension-ality of the data is determined by the pulse program. If this contains an if and/or st statement, zg assumes a 2D or 3D dataset. Furthermore, if the pulse program contains a nested loop with loop counters td1 and td2, zg assumes a 3D data-set. Finally, the acquisition parameter PARMODE is evaluated. If the value of PARMODE is not consistent with the pulse program, zg will display a warning but allow you to continue the acquisition. 1D data are stored a file named fid under the experiment number (expno) of the current dataset. 2D and 3D data are stored in a file named ser in the same directory. At the time of this writing, XWIN-NMR supports 1D, 2D and 3D datasets. However, the pulse program is not limited to 3D and allows you to acquire data in 4 or more dimensions. The re-sulting raw data (the ser file) can be processed by third party software that sup-ports 4 or more dimensions. The parameters for the fourth and higher dimensions must be created manually.

Normally, an acquisition will run until it has finished. If, however, you want to interrupt it, you can do that with the command halt. This will finish the current scan, write the data to disk and then stop the acquisition. Note that halt finishes the current scan but not the current phase cycle. The command stop immedi-ately stops the acquisition. It does not finish the current scan or write the data to disk. Instead of entering stop, you can also click the stop button. If, for some reason, halt and stop do not work, you can use the command kill to stop the acquisition.

When an acquisition has finished but you find out that the signal to noise is in-sufficient, you can accumulate additional scans. Just set the parameter NS to the number of extra scans and enter go. This command does not overwrite the ex-isting data but adds the extra scans to them. Caution: go works correctly if the previous acquisition has finished normally but should not be used if this has been interrupted with halt or stop (see the description of go).

zg overwrites possibly existing raw data. Each user can configure XWIN-NMR to


DONE

INDEX

INDEX

get a warning about existing data or not. Enter the command setres and set the flag ZGsafety to on to get a warning. Note the difference between zg an go. The latter command does not overwrite existing data but adds new data to them.

After a manually performed acquisition has finished, it is normally processed with processing commands like em, ft, apk etc. This will automatically switch the display to the processing menu (if it wasn’t already there) and show you the spectrum. Processing commands are described in the Processing Reference Manual.

The command zg is automatically executed by AU programs that contain the ZG macro. Examples of these are au_zg*, au_getl* and multizg. Fur-thermore, zg is automatically executed when experiments are started from the automation interfaces ICON-NMR and buttonnmr.

Note that an acquisition always runs in background which means that XWIN-NMR can do other tasks simultaneously. You can change the display to a different dataset and process data there. This is actually what happens all the time during an automation sequence performed by ICON-NMR.

XWIN-NMR is supplied with a large number of pulse programs from simple 1D to sophisticated multidimensional experiments. Furthermore, you can write your own pulse programs with the edpul command using the Bruker pulse programs as an example. For a detailed description of the pulse program syntax click:


INPUT PARAMETERS

all acquisition parameters as described in chapter 2

OUTPUT PARAMETERSall acquisition status parameters as described in chapter 2

INPUT FILES1D data



2D data


DONE

INDEX

INDEX


acqu - acquisition parameters direct dimension (F2) acqu2 - acquisition parameters indirect dimension (F1)

3D data


acqu - acquisition parameters direct dimension (F3) acqu2 - acquisition parameters indirect dimension (F2) acqu3 - acquisition parameters indirect dimension (F1)

All data

<xwhome>/exp/stan/nmr/lists/pp

<PULPROG> - the pulse program defined by PULPROG

<xwhome>/conf/instr/<curinst>/

scon - spectrometer parameters (created with edscon)

OUTPUT FILES1D data


fid - raw dataacqus - acquisition status parameters

2D data


ser - raw dataacqus - acquisition status parameters direct dimension (F2)acqu2s - acquisition status parameters indirect dimension (F1)

3D data


ser - raw dataacqus - acquisition status parameters direct dimension (F3) acqu2s - acquisition status parameters indirect dimension (F2)acqu3s - acquisition status parameters indirect dimension (F1)


DONE

INDEX

INDEX

All data


pulseprogram - the precompiled pulse programaudita.txt - acquisition audit trailscon - spectrometer parameterscpdprg1 - CPD program (output if a cpd1:f2 statement is used)cpdprg2 - CPD program (output if a cpd2:f2 statement is used).etc.fq1list - variable frequency list (output if a fq1 statement is used)fq2list - variable frequency list (output if a fq2 statement is used)ect.spnam1 - shaped pulse definition (output if a sp1 statement is used)spnam2 - shaped pulse definition (output if a sp2 statement is used)ect.gpnam1 - shaped gradient definition (output if a gp1 statement is used)gpnam2 - shaped gradient definition (output if a gp2 statement is used)ect.vclist - variable counter list (output if a vc statement is used)vdlist - variable delay list (output if a vd statement is used)vplist - variable pulse list (output if a vp statement is used)dslist - dataset list (output if a wr #n or wr ## statement is used)cag_par - rotation matrices for gradients used for imaginggrdprog - shaped gradient definition (output if a ngrad statement is used)

USAGE IN AU PROGRAMSZG

SEE ALSO

go, gs, rga, wobb, atma, suspend, resume

A-227

Chapter 10

Temperature commands

This chapter describes commands which configure, control or monitor the temper-ature unit. A temperature unit which are delivered with Bruker spectrometers is often referred to as a eurotherm; the make of most units. They are used to warm up or cool down the NMR sample and keep it at a certain temperature during the experiment.

A-228 Temperature commands

DONE

INDEX

INDEX

edte

NAMEedte - edit the temperature parameters

DESCRIPTIONThe command edte opens a dialog box from which the temperature unit can be controlled. The functionality of this window is described in a separate manual that can be opened from the XWIN-NMR window by clicking Help � Other top-ics � Temperature regulation or from the edte window by clicking Help � Edte Users Manual

SEE ALSOedtg, tepar, temon, teget, te2get, teset, te2set, teready, te2ready

Temperature commands A-229

DONE

INDEX

INDEX

edtg

NAMEedtg - edit the temperature parameters for gradient temperature units

DESCRIPTIONThe command edtg opens a dialog box from which the gradient temperature unit can be controlled. The functionality of this window is described in a sepa-rate manual that can be opened from the edtg window by clicking Help � Edtg Users Manual

SEE ALSO

edte, tepar, temon, teget, te2get, teset, te2set, teready, te2ready


DONE

INDEX

INDEX

teget, te2get

NAMEteget - get the temperature from the temperature unitte2get - get the second temperature from the temperature unit

DESCRIPTION

The command teget gets the temperature from the temperature unit and stores it in the acquisition status parameter TE.

te2get gets the so called second temperature from a temperature unit with two regulators. The value is stored in the acquisition status parameter TE2. Temper-ature units with two regulators are, for example, used in BEST NMR where the first regulator controls the sample temperature and the second regulator controls the inlet capillary temperature.

OUTPUT PARAMETERSTE - demand temperate on the temperature unitTE2 - demand second temperate on the temperature unit

OUTPUT FILES



USAGE IN AU PROGRAMSTEGET

TE2GET

SEE ALSOedte, tepar, temon, teset, te2set, teready, te2ready


DONE

INDEX

INDEX

temon

NAMEtemon - temperature monitor

DESCRIPTIONThe command temon opens a temperature monitor window which shows:

• the last measured temperature

• the time the last temperature was measured

• the minimum and maximum temperature since temon was started

The temon window offers the following buttons:

Mode - switches the display mode and shows the maximum and minimum tem-perature and the time at which they were measured

Celsius/Kelvin - switches between Celsius and Kelvin

LogFileopens a new window with the following buttons:

Write log file ON/OFF a radio button which allows you to switch on/off the writing to a log file

Time Intervalallows you to set the interval in which the logfile is updated. A list of possible time intervals appears and you must double click a value to select it.

print log fileprints the log file to the system default printer

OKcloses the LogFile window

Close - close the temon window

A graphical temperature monitor can be started by clicking:

Data � Monitor temp. & Output Power

from the edte dialog window.


DONE

INDEX

INDEX

OUTPUT FILES

<userhome>/.xwinnmr-<hostname>/

temon - last measured temperature


temperatureLog - temperatures measured at regular intervals

SEE ALSOedte, edtg, tepar, teget, te2get, teset, te2set, teready, te2ready


DONE

INDEX

INDEX

tepar

NAMEtepar - get a predefined set of temperature unit parameters

SYNTAXtepar [<name>]

DESCRIPTION

The command tepar gets a predefined set of temperature unit parameters. These are parameters which have been previously stored from the edte window by clicking File � Save configuration.

The command tepar takes one argument and can be used in one of the follow-ing ways:

teparshows a list of available temperature parameter sets. When you click one, it is loaded to the temperature unit.

tepar <name.tcf>loads the temperature parameter set <name> to the temperature unit.

INPUT FILES<xwhome>/exp/stan/nmr/lists/eurotherm/tcf/*

temperature parameter sets


TEPAR(filename)

SEE ALSOedte, edtg, temon, teget, te2get, teset, te2set, teready, te2ready


DONE

INDEX

INDEX

teready, te2ready

NAMEteready - wait until the temperature set with teset has been reachedte2ready - wait until the temperature set with te2set has been reached

SYNTAX

teready <stabilization time> <precision>te2ready <stabilization time> <precision>

DESCRIPTIONThe command teready waits until the demand temperature has been within the specified precision range for at least 10 seconds. If this does not happen with-in the specified stabilization time, teready terminates. teready is typically executed after setting the target temperature with the command teset. For ex-ample, the command sequence:

teset 320.0teready 300 0.5

sets the temperature to 320.0 K and waits until this has been reached approxi-mately. More precisely, it waits until the temperature has been between 319.5 and 320.5 for at least 10 seconds. After that, teready waits another 300 sec-onds to allow for temperature stabilization of the sample.

The stabilization time (in seconds) and precision (in Kelvin) must be specified as arguments, they are not prompted for it they are omitted.

te2ready works like teready except that it controls the so called second tem-perature on a temperature unit with two regulators. These units are, for example, used in BEST NMR where the first regulator controls the sample temperature and the second regulator controls the inlet capillary temperature.

USAGE IN AU PROGRAMSTEREADY(time, precision)

TE2READY(time, precision)


DONE

INDEX

INDEX

SEE ALSO

edte, edtg, tepar, temon, teget, te2get, teset, te2set


DONE

INDEX

INDEX

teset, te2set

NAMEteset - set the temperature on the temperature unitte2set - set the second temperature on the temperature unit

SYNTAX

teset [<temperature>]te2set [<temperature>]

DESCRIPTIONThe command teset sets the temperature on the temperature unit. It takes one argument and can be used as follows:

tesetsets the temperature to the value of the acquisition parameter TE. Before you en-ter teset without argument you must set TE to the desired temperature, in Kel-vin, either from eda or by typing te on the command line.

teset <temperature>sets the temperature to the specified value.

The command teset is, for example, used in the AU programs au_zgte and multi_zgvt.

te2set works like teset except that it sets the so called second temperature to the value of the acquisition parameter TE2. This value is set on the second reg-ulator of a

temperature unit with two regulators. Such units are, for example, used in BEST NMR where the first regulator controls the sample temperature and the second regulator controls the inlet capillary temperature.

INPUT PARAMETERS

TE - demand temperature on the temperature unit (input of teset)TE2 - demand temperature on the temperature unit (input of te2set)



DONE

INDEX

INDEX


USAGE IN AU PROGRAMSTESET

TE2SET

VT executes the command teset <list_index>

SEE ALSOedte, edtg, tepar, temon, teget, te2get, teready, te2ready

A-239

Chapter 11

MAS/Solids commands

This chapter describes commands which are used for solid state experiments. In most of them magic angle spinning is used. As such, most of the commands described here concern the control of the MAS pneumatic unit. Furthermore, com-mands for controlling the high power control unit (HPCU) are described. Note that this unit is used on Avance-AQX but not on Avance-AQS. On the latter, the HPCU commands are obsolete.

A-240 MAS/Solids commands

DONE

INDEX

INDEX

cfmas

NAMEcfmas - configure the MAS pneumatic unit

DESCRIPTIONThe command cfmas allows you to configure the MAS pneumatic unit. It will prompt you for the rs232 channel and for the following information:

• Minimum main pressure (default 4000 mBar)

• Insert air on time (default 10 sec)

• Eject air on time (default 10 sec)

• Sample diameter (Wide or Normal)This actually concerns the type of eject mechanism. For probes with a tilting stator you must enter N(ormal), for probes with a fixed stator W(ide).

• SpinLock tolerance (default 5 Hz)For solid state MAS, the default value of 5 Hz can be accepted. For HR MAS, a value between 5 and 90 must be entered. The Spinlock tolerance refers to the required precision of the demand spin rate. If, for example, you specify 10 Hz and turn on the spinning, the spin rate will be adjusted until it has reached the demand spin rate plus or minus 10 Hz and stayed there for at least 5 seconds.

cfmas can also be executed as a part of the XWIN-NMR configuration suite (command config). When a hardware list is used (see cf), the MAS unit can be specified there. In that case, the command cfmas is not needed because the MAS unit is configured by cf.



mas - serial port for MAS unit


mas_params - MAS parameters

MAS/Solids commands A-241

DONE

INDEX

INDEX

SEE ALSO

cf, config, mas, mascontrol, masr, masi, masg, mash, mase


DONE

INDEX

INDEX

edhpcu

NAMEedhpcu - edit the acquisition plus HPCU parameters

DESCRIPTIONThe command edhpcu opens a dialog window with all acquisition parameters and all HPCU parameters. The former corresponds to the eda parameters. The latter involve the gain parameters HGAIN1 to HGAIN4 and XGAIN1 to XGAIN4 and the tune parameters TUNHIN, TUNHOUT and TUNXOUT.


all acquisition parameters and the following HPCU parameters:

HGAIN1 - HGAIN4 - gain level 1- 4 for 1H/19F tube transmitter XGAIN1 - XGAIN4 - gain level 1- 4 for X nucleus tube transmitterTUNHIN -1H/19F high power tube transmitter input tuningTUNHOUT -1H/19F high power tube transmitter output tuningTUNXOUT - X nucleus high power tube transmitter output tuning




SEE ALSO gethpcu, sethpcu, rackpow


DONE

INDEX

INDEX

ed4ph

NAMEed4ph - edit the 4-phase modulator parameters

DESCRIPTIONThe command ed4ph opens a dialog box where you can set the parameters for the 4-phase modulator. This unit is mainly used for solid state experiments. This allows for a much faster 90° phase switching (+x, +y, -x, -y).

The following parameters are offered:

FX_AX - F1 channel amplitude of +x

FX_AMX - F1 channel amplitude of -x

FX_PY - F1 channel phase of +y

FX_PMY - F1 channel phase of -y

FX_AY - F1 channel amplitude of +y

FX_AMY - F1 channel amplitude of -y

FX_PMX - F1 channel phase of -x

For the F2 channel, the corresponding parameters are called FH_*. For the F3 channel, the corresponding parameters are called FY_*. Note that not all spec-trometers are equipped with the F3 channel. Furthermore, some spectrometers do have an F3 channel but no 4-phase modulator because the frequency is direct-ly created on the synthesizer.

RECPHASE - receiver phase

When you enter a value in any of the above parameters and hit the return key, the entered value is immediately set on the 4-phase modulator.

At the bottom of the dialog box, the following push buttons are available:

QUITcloses the dialog box

LISTunused


DONE

INDEX

INDEX

SaveToFileallows you to store the current values to disk. A list of existing file appears or you can enter a new filename.

LoadParFileallows you to read a previously stored values from disk. A list of existing file appears.

ReadAllParunused

The regular way of phase switching, as it occurs in most high resolution exper-iments, is the use of a phase program like:

ph1 = 0 90 180 270

The phases are provided by the spectrometer FCU and require a certain time to be set, typically 3µsec. If you replace this phase program by the following one:

ph1 = +x +y -x -y

the same phase cycle is used but now the phases are provided by the 4-phase modulator. The switching time is now as short as 50nsec.

The 4-phase modulator can be use with or without an HPCU. In the former case, it must be connected to the 4-PH connector of the HPCU. In the latter case, it must be connected to the second rs485 channel of the CCU and must be speci-fied in the hardware list (see also cf). Note that spectrometers which are equipped with transistorized amplifiers rather than tube amplifiers are not equipped with (and do not need) an HPCU.

The 4-phase modulator can only be used for hard pulses, not for shaped pulses. On Avance-AQS spectrometers, the 4-phase modulator is not needed and, as such, not supported. The reason is that the frequency generation on the SGU doesn’t cause any phase switching delays.

OUTPUT FILES/xwhome/exp/stan/nmr/lists/4ph/

SEE ALSO

edhpcu


DONE

INDEX

INDEX

mas

NAMEmas - open the MAS control window

DESCRIPTIONThe command mas opens a dialog box where you can set the MAS parameters and control the pneumatic unit. The following entries are available:

Probe Setup Filename

shows a list of available MAS parameter files. These are files that have been stored previously from the mas window and contain the probehead type.

Bearing Gas Port

This button is only used for the older heat exchanger types that use 3 input lines. It allows you to select demand temperature. Possible values are Am-bient (default), -70°C or -120°C. After selecting a temperature, this is set on the pneumatic unit.

Probehead Selection

a set of toggle buttons that allow you to set the following parameters:

• Diameter: sample diameter

• Probe; probehead type

• Type: magnet type, used to define tilt or no tilt of the stator (seeInsert sample below)

• Material: rotor material

• User: unused

Clicking these buttons will toggle between their possible values. Only values that correspond to existing hardware are available. Together, the selected values will determine the algorithms that are used to spin the sample. When you enter mas, the current values are read from the MAS pneumatic unit.

Main Pressure, Bearing Pressure, Drive Pressure, Spin Rate


DONE

INDEX

INDEX

Each of these parameters shows three values:

Demand: field showing the current demand value. If you enter a new val-ue, this is set on the pneumatic unit.

Actual: push buttons showing the actual value on the pneumatic unit. Note that they are only updated when clicked. They are, however, contin-uously updated, if the button ContinuousUpdate is highlighted

Maximum: not implemented.

The parameters are read from the MAS pneumatic unit when you enter the mas command. See also Setting Mode.

Setting Mode

The MAS unit can work in two different modes:

Manual modeyou must enter the Bearing Pressure and Drive Pressure. The Spin Rate will be automatically adjusted.

Automatic mode you must enter the Demand Spin Rate. The Drive pressure and Bearing Pressure will be automatically adjusted.

Spinning

Allows you to switch the spinning on or off. Caution: after entering the Insert Sample command (see below), you must wait at least the time specified by Insert Airtime before you switch on the spinning.

Spin Locked

Status flag that indicates whether or not the spin rate is locked. Spin Locked is automatically set to yes when the spin rate has reached the de-mand spin rate within a range of plus or minus 5 Hz and stayed there for more than 5 seconds. Spin Locked only works in Automatic mode.

StartupProgram

Unused. It is automatically defined by Probehead Selection (see above).

Insert Air Time

Allows you to modify the Insert Air Time. By default, the value that was set with cfmas is used. Note that the value entered here is not stored on


DONE

INDEX

INDEX

disk. When you exit the mas window, it is set back to the value that was entered with cfmas.

Eject Air Time

Allows you to modify the Eject Air Time. By default, the value which was set with cfmas is used. Note that the value entered here is not stored on disk. When you exit the mas window, it is set back to the value that was entered with cfmas.

Insert sample

Before you click this button you must insert the spinner into the sample transfer tube.The effect depends on the probehead type. For standard bore probes, which tilt the stator for sample change, a period specified by Insert Airtime is waited and then the stator is tilted back to the magic angle. For probes where the stator is not tilted (all wide bore and some standard bore probes) an air flow through the insert line pushes the spinner into the sta-tor. Standard bore probes that are not tilted are for example, all probes with 2.5 mm diameter and all probes for spectrometer ≥ 700 MHz.

Eject sample

ejects the sample from the stator. Before you click this button, you must stop the spinning.

Continuous Update

causes the parameters Main Pressure, Bearing Pressure, Drive Pressure and Spin Rate to be continuously updated, i.e. read from the MAS pneu-matic unit.

Save

saves the current parameters to a Probe Setup Filename

Edit

allows you to edit Probe Setup Files

List

unused

Cancel

exits the mas dialog box.


DONE

INDEX

INDEX

INPUT FILES

<xwhome>/exp/stan/nmr/lists/mas/

Probe Setup Files (input of mas � Probe Setup Filename)


mas_params - MAS parameters

OUTPUT FILES<xwhome>/exp/stan/nmr/lists/mas/

Probe Setup Files (output of mas � Save)

SEE ALSO

mascontrol, cfmas, masrmon, masr, masi, masg, mash, mase


DONE

INDEX

INDEX

mascontrol

NAMEmascontrol - open the MAS monitor and control window

DESCRIPIONThe command mascontrol opens a dialog box where you can set the MAS parameters and monitor the MAS pneumatic unit. It can be used as an alternative to the commands mas and masrmon.

mascontrol starts by opening a small window where you can select the probehead. After doing that, a new window appears where the current MAS spin rate is displayed and the following buttons are available:

Mode

When you click this button, the MAS spin rate is shown and new additional buttons will appear:

insert (for wide bore probes and standard bore probes without stator tilt)Before you click this button, you must insert the spinner into the sample transfer tube.The action of insert depends on the probehead type. For standard bore probes, which tilt the stator for sample change, insert waits a period specified by Insert Airtime and then tilts the stator back to the magic angle. For probes where the stator is not tilted (all wide bore and some standard bore probes), insert causes an air flow through the insert line that pushes the spinner into the stator.

set angle (for standard bore probes with stator tilt)See insert.

ejectejects the sample from the probehead. It switches the air flow on for a time which has been defined with cfmas.

startbrings the sample rotation up to the demand spin rate.

stopstops sample rotation.


DONE

INDEX

INDEX

etc.

When you click this button, a new window appears with the radio button:

Write log file ON/Write log file OFFswitches the writing of the log file on/off. The log file is stored under the EXPNO of the dataset where mascontrol was started.

and the following push buttons:

Screen Updateallows you to set the screen update interval (seconds). A list of possible time intervals appears and you must double click a value to select it.

Logfile time intervalallows you to set the interval at which the logfile is updated. A list of pos-sible time intervals appears and you must double click a value to select it.

Select new probeopens a new window with all available probeheads will appear. When you click one, the mas dialog window will be opened where you can read a new Probehead Setup Filename or select a new probehead.

Set new spin rateopens a new dialog window where you can change the spin rate.

Show log fileshows the MAS log file on the screen.

Print log fileprints the log file on the system default printer.

INPUT AND OUTPUT PARAMETERScan be viewed with dpa or by typing 1s masr :


INPUT FILES

<xwhome>/prog/tcl/xwish3_scripts/

mascontrol - mascontrol Tcl/Tk startup script




DONE

INDEX

INDEX

OUTPUT FILES


acqus - acquisition status parameters masRateLog - spin rate log file

SEE ALSO

mas, masrmon, cfmas, masr, masi, masg, mash, mase


DONE

INDEX

INDEX

masr, masi, masg, mash, mase

NAMEmasr - set the spin ratemasi - insert the spinnermasg - start spinningmash - halt the spinnermase - eject the spinner

DESCRIPTION

MAS control like sample insert and eject, sample rotation etc. is usually done from one of the MAS control windows (commands mas or mascontrol). It can, however, also be done with the commands described on this page.

masr Prompts you for the demand spin rate and then sets the specified value on the MAS pneumatic unit. It also sets the acquisition parameter MASR.

masr getreads the actual spin rate from the pneumatic unit and stores it into the acqui-sition status parameter MASR.

masr acqusets the demand spin rate on the MAS pneumatic unit according to the acqui-sition parameter MASR.

masiBefore you enter this command you must insert the spinner into the sample transfer tube.The action of masi depends on the probehead type. For standard bore probes, which tilt the stator for sample change, masi waits a period spec-ified by Insert Airtime and then tilts the stator back to the magic angle. For probes where the stator is not tilted (all wide bore and some standard bore probes), masi causes an air flow through the insert line that pushes the spinner into the stator.

masg Starts the sample rotation according to the demand spin rate.

masg wait shows the values of Lock Status (LoSt), Spin Rate (VA), Driver Pressure (PD) Bearing Pressure (PB), Bearing Sense Pressure (PS). It blocks


DONE

INDEX

INDEX

all other MAS commands until Lock Status is 1. It is typically used in auto-mation (see the macro MASG below).

mash Stops the sample rotation.

mash wait does the same but blocks all other MAS commands until the spin rate has become zero. It is typically used in automation (see the macro MASH below).

maseEjects the sample from the probehead. It switches the air flow on for a time which has been defined with cfmas.

Note that all these commands, except for masr get, are ignored when an ac-quisition is running. No error message is displayed.

More information on MAS is available in some manuals which can be opened from XWIN-NMR by clicking Help � Other topics:

� Solids Users Manual

� Help � Other topics � SB/MAS Manual

� BASH spectrometer documentation

Note that the last manual requires the BASH CDROM.

INPUT PARAMETERS

MASR - MAS spin rate (input of masr acqu)

OUTPUT PARAMETERSMASR - MAS spin rate (acquisition status parameter, output of masr get)MASR - MAS spin rate (acquisition parameter, output of masr)

INPUT FILES




mas_params - MAS parameters (input of masi and mase)


DONE

INDEX

INDEX


MASI

MASE

MASRexecutes the command masr acqu

MASRGET executes the command masr get

MASH executes the command mash wait

MASG(retries)executes the command masg wait n, where n is the number of retries

SEE ALSOcfmas, mas, mascontrol, masrmon


DONE

INDEX

INDEX

masrmon

NAMEmasrmon - monitor the MAS spin rate

DESCRIPTIONThe command masrmon monitors the MAS spin rate. It opens a dialog box with the following buttons:

LogFileopens a new window with the following buttons:

Write log file ON/OFF a radio button which allows you to switch on/off the writing to a log file

Time Intervalallows you to set the interval in which the logfile is updated. A list of possible time intervals appears and you must double click a value to select it.

print log fileprints the log file to the system default printer

OKcloses the LogFile window

Modeallows you to toggle between the following display modes:

• the mode showing the current spin rate

• the mode showing the current, maximum and minimum spin rate and the times at which they occurred.

Closecloses the MAS monitor window

OUTPUT PARAMETERS

can be viewed with dpa or by typing 1s masr :



DONE

INDEX

INDEX

OUTPUT FILES


acqus - acquisition status parametersmasRateLog - spin rate log file

SEE ALSO

mas, mascontrol, cfmas, masr, masi, masg, mash, mase


DONE

INDEX

INDEX

rackpow, gethpcu, sethpcu

NAMErackpow - switches the high power cabinet on/off gethpcu - reads the gain and I/O tuning values of tube amplifiers from the HPCUsethpcu - sets the gain and I/O tuning values of tube amplifiers on the HPCU

DESCRIPTIONThe command rackpow switches the high power cabinet on or off. This is done according to the acquisition parameter POWMOD. For POWMOD = low, it is switched off, for POWMOD = high, it is switched on.

The command gethpcu reads the gain from the HPCU and stores them into the acquisition parameters HGAIN1 to HGAIN4, XGAIN1 to XGAIN4. Further-more, it reads the I/O tuning values of tube amplifiers from the HPCU and stores them into the acquisition parameters TUNHIN, TUNHOUT and TUNXOUT.

The command sethpcu sets the gain from the HPCU according to the acqui-sition parameters HGAIN1 to HGAIN4, XGAIN1 to XGAIN4. Furthermore, it sets the I/O tuning values of tube amplifiers on the HPCU according to the ac-quisition parameters TUNHIN, TUNHOUT and TUNXOUT.


HGAIN1 - HGAIN4 - gain level 1-4 for the 1H/19F tube transmitter XGAIN1 - XGAIN4 - gain level 1-4 for the X nucleus tube transmitterTUNHIN -1H/19F high power tube transmitter input tuningTUNHOUT -1H/19F high power tube transmitter output tuningTUNXOUT - X nucleus high power tube transmitter output tuning


acqu - acquisition parameters (input for rackpow and sethpcu)


acqu - acquisition parameters (output of gethpcu)


DONE

INDEX

INDEX


RACKPOWSETHPCUGETHPCU

SEE ALSO

edhpcu

A-259

Chapter 12

Rename and delete commands

This chapter describes XWIN-NMR commands which allow you to rename or delete acquisition related files. These include parameter sets, pulse programs, gradient programs shim sets, AU programs, XWIN-NMR macros and various lists.

A-260 Rename and delete commands

DONE

INDEX

INDEX

delpar, delpul, delgp, delsh, delau, delmac

NAMEdelpar - delete parameter sets delpul - delete pulse programs delgp - delete gradient programs delsh - delete shim files delau - delete AU programsdelmac - delete macros

SYNTAXdelpar [<name>]

delpul, delgp, delsh, delau and delmac have the same syntax as delpar

DESCRIPTION

The command delpar displays a list of parameter sets, both Bruker and user defined. Each entry shows the parameter set name and the parameter types in that set. You can mark one or more parameter sets for deletion and then click Execute to actually delete them. Furthermore, you can print the list by clicking the Print button. If you have accidentally removed Bruker parameter sets, you can re-install them with the command expinstall.

The other del* commands mentioned here all work like delpar, deleting the type of files as specified above. Note that delau deletes both the selected AU source files and the corresponding executable files. If you accidentally delete Bruker AU programs, pulse programs or gradient programs, you can re-install them with expinstall. In case of AU programs, you must also compile them with cplbruk or xau.

INPUT FOLDERS

<xwhome>/exp/stan/nmr/par - Bruker and user defined parameter sets

<xwhome>/exp/stan/nmr/lists/pp - Bruker and user defined pulse programs

<xwhome>/exp/stan/nmr/lists/gp - Bruker and user defined gradient programs

<xwhome>/exp/stan/nmr/lists/bsms - shim files

<xwhome>/exp/stan/nmr/lists/mac - Bruker and user defined macros

Rename and delete commands A-261

DONE

INDEX

INDEX

<xwhome>/exp/stan/nmr/au/src - Bruker and user defined source AU programs

<xwhome>/prog/au/bin - Bruker and user defined binary AU programs

<xwhome>/exp/stan/nmr/lists/mac - Bruker and user defined macros


DELPAR(name)

No AU macros are available for the other del* commands.

SEE ALSOdellist


DONE

INDEX

INDEX

dellist

NAMEdellist - delete various lists

SYNTAXdellist [<name>]

DESCRIPTION

The command dellist displays a list of various lists types. Most of them are used in acquisition, e.g. vd lists contain variable delays which are read by the vd statement in pulse programs. When you click a list type, the available files of that type appear. You can click individual entries to mark them for deletion or click the button Select all. Clicking the Execute button deletes all marked entries.

All lists which appear with dellist can be printed by clicking the Print but-ton.

INPUT FILES<xwhome>/exp/stan/nmr/lists

pp - pulse programscpd - CPD programsgp - gradient programsds - dataset listsvc - variable counter listsvd - variable delay listsvp - variable pulse lists vt - variable temperature listsf1 - frequency listsf2, f3 - frequency lists (A*X spectrometers only)mac - XWIN-NMR macrosroi - 2D integral rangesscl - scaling region filesmasr - MASR rotation values


DONE

INDEX

INDEX

SEE ALSO

delpar, delpul, delgp, delsh, delau, delmac


DONE

INDEX

INDEX

renau, renpar

NAMErenau - rename AU programsrenpar - rename parameter sets

DESCRIPTION

The command renau opens a dialog box with all AU programs, both Bruker and user defined. You can rename one or more AU programs, simply by replac-ing their names. When you enter a new name and press the Enter key, the AU program is immediately renamed. This counts for both the source and the binary file. The dialog box can be closed by clicking Cancel.

renpar works like renau, except that it allows you to rename parameter sets. Parameter sets are directories, so renpar changes directory names; the names of the parameter files in those directories (acqu, proc, meta, outd) are not affect-ed.


For renau:

<xwhome>/exp/stan/nmr/au/src/*<xwhome>/prog/au/bin/*

For renpar:

<xwhome>/exp/stan/nmr/par/*

SEE ALSOrengp, renlist, renlut, renmac, renpul


DONE

INDEX

INDEX

renpul, rengp, renlut, renmac

NAMErenpul - rename pulse programsrengp - rename gradient programsrenlut - rename 2D lookup tablesrenmac - rename macros

DESCRIPTIONThe command renpul opens a dialog box with all pulse programs, both Bruker and user defined. You can rename one or more pulse programs, simply by replac-ing their names. When you enter a new name and hit the Enter key, the pulse program is immediately renamed. The dialog box can be closed by clicking Can-cel.

In the same way, rengp, renlut and renmac allow you to rename, gradient programs, 2D lookup tables and macros respectively.


<xwhome>/exp/stan/nmr/lists/pp/*

pulse programs

<xwhome>/exp/stan/nmr/lists/gp/*

gradient programs

<xwhome>/exp/stan/nmr/lut/*

2D lookup tables

<xwhome>/exp/stan/nmr/lists/mac/*

XWIN-NMR macros

SEE ALSOrenlist, renau, renpar


DONE

INDEX

INDEX

renlist

NAMErenlist - rename various lists

DESCRIPTIONThe command renlist displays a list with various lists types, most of which are used in acquisition. When you click a list type, a dialog box appears with the available entries of that type. You can rename one or more entries, simply by re-placing their names. When you enter a new name and hit the Enter key, the list is immediately renamed. The dialog box can be closed by clicking Cancel.

INPUT AND OUTPUT FILES<xwhome>/exp/stan/nmr/lists/*

SEE ALSOrenau, renpar, rengp, renlut, renmac, renpul

A-267

Chapter 13

Miscellaneous

This chapter describes XWIN-NMR commands that are somehow acquisition related and have not been described in previous chapters.

A-268 Miscellaneous

DONE

INDEX

INDEX

pulsdisp

NAMEpulsdisp - open the pulse program display

DESCRIPTIONThe command pulsdisp simulates the pulse sequence and shows it in a graph-ical representation. It uses the pulse program of the current dataset as it is de-fined by the acquisition parameter PULPROG. The graphical representation includes the pulse program timing, frequencies, phases and power levels.

The pulse program display can be started by entering pulsdisp on the com-mand line or click Windows � Pulse program. First a small window will appear where you can select the length of the simulation and the elements to be dis-played. the following fields/buttons are available:

• Observe Setup This button to select the elements to be displayed. A new window will appear fro which you can select the elements to be displayed. The following check buttons are available:

CHnselect the pulse channels to be displayed

FCUnselect the frequency unit for which you want to display the phases and/or power levels

GCUX, GCUY, GCUZselect the X,Y and/or Z gradient output to be displayed

RCUGOselect receiver control to be displayed

Receiver display the receiver status (on/off) and receiver phase

Progshow the pulse program statement for each time segment

Apply store the current settings of the Observe Setup window

Miscellaneous A-269

DONE

INDEX

INDEX

OKstore the current settings of the Observe Setup window and quit

• Time/Scans allows you to choose between the display of a certain time interval or a cer-tain number of scans.

• Start and Stop allows you to enter the simulation starting point and end point, respectively. The entered values will be interpreted as time values, if you selected Time in the previous step and as scan numbers if you selected Scans. You can also specify a negative number to simulate dummy scans. This, however, only works if the acquisition parameter DS is set to a positive value. If you checked one or more FCUn channels in the Observe Setup window, then the value in the Start field will be ignored. In that case, the simulation will always start with the first scan (scan 0 or time 0.0).

• Run simulationstarts the simulation. This usually takes a few seconds, depending on the pulse sequence and selected time interval or number of scans. When the simulation is finished, a new window will appear showing the graphical rep-resentation of the pulse sequence: the actual pulse program display. This consists of one row for each element that was selected in the Observe Setup window. You will see the exact timing of the entire sequence including the implicit delays that, for example, occur in the statement go=n. The follow-ing buttons are available:

Setup display: clicking this button will open a new dialog box that is equivalent to the one opened by Observe Setup. It allows you to change the simulation selection, for the current simulation window. It will not af-fect the selection for possible other simulation windows nor does it affect the selection in the original Observe Setup window.

Zoom in allows you to investigate the fine details of the pulse sequence. Particular-ly text labels indicating the length of durations, power levels in db or per-cent units, phases in degrees, or pulse program text will only appear after you zoom. Note that the timing sequence also shows the so called implicit delays. These are delays which do not appear as such in the pulse program but are introduced by statements like go=n.

Zoom out

A-270 Miscellaneous

DONE

INDEX

INDEX

allows you to undo the effect of Zoom in and get an overview of the entire simulation.

New display allows you to open an extra pulse display window which is a copy of the first one. You can, for example, use one window to zoom in and the other for an overview.

Kill display allows you to close the current pulse display window.

Printallows you to print the current pulse display window. A dialog box will be opened where you can print, print to file, preview the print and setup the printer. Note that, for a long simulation, you might want to use multiple sheets of paper. You can specify this in the Split to X*Y Pages field in the Setup window.

If you checked one or more FCUn simulations in the Observe Setup window, and the pulse program has many phase changes, the simulation time might take very long. Furthermore, it can happen that the available memory limit is exceeded or the graphics gets too large and will be truncated (an error mes-sage will appear if this happens).

• New Display

• Show programshow the contents of the pulse program

• Undo undo the last change

• Quitquit the pulse program display

The pulse display startup window also offers the following menu:

• File

Quitquite the pulse program display (same as the Quit button)

• View

New display

Kill displays

Miscellaneous A-271

DONE

INDEX

INDEX

Align displays

• Options

Scale setupallows you to select the time axis scaling mode; cut or logarithmic. cut scaling will result in a true representation of all duration in the pulse pro-gram shorter than the time constant TC. Durations that exceed TC, it will be represented with thick solid lines. TC can be specified in the field Time constant. Logarithmic scaling will cause a compressed representation of all durations. Nevertheless, since pulse lengths are usually a in the range of microseconds and delays in the range of milliseconds or seconds, a log-arithmic representation can give a better overview.

Observe setup same as the Observe setup button described above

FCU simulator setupallows you to select the pulse power units (db, a logarithmic unit, or %, a linear unit).

Printer setupallows you to select the printer and setup the print parameters for printing the pulse program display window.

• HelpPulse program display Quick-Start Guide

If you change acquisition parameters or the pulse program while the pulse pro-gram display is open, you must quit and restart it. Just clicking New display or even Run simulation again will not account for the change.

INPUT FILES

<xwhome>/prog/app-defaults

PulseDisplay - pulse program display resources

SEE ALSO spdisp

A-272 Miscellaneous

DONE

INDEX

INDEX

spdisp

NAMEspdisp - symbolic (graphical) pulse program display

DESCRIPTIONThe command spdisp opens a new window with a symbolic pulse program display. It takes one argument and can be used as follows:

spdispdisplays the pulse program defined by the acquisition parameter PULPROG

spdisp <name>displays the pulse program <name>

spdisp starts the pulse program display part of NMR-SIM. The functionality of the program is described in the NMR-SIM manual. This can be opened by clicking Help from the window that is opened by spdisp. I

spdisp actually starts the AU program showpp, which, in turn, calls the pulse program display of the NMR-SIM program. The following commands are equiv-alent:

spdisp <name>showpp <name>nmrsim -showp <name>

spdisp can only start if the following conditions are met:

• the Bruker AU programs have been installed (with expinstall)

• the NMR-SIM program is installed (from the NMR Suite CDROM)

The difference between spdisp and pulsdisp is the following. spdisp gives a graphical representation of the pulse sequence and is well suited for desktop publishing. pulsdisp shows the pulse sequence in much greater de-tail and is primarily useful for the investigation of new pulse sequences.

INPUT FILES<xwhome>/exp/stan/nmr/au/

showpp - AU program started by spdisp (source file)

Miscellaneous A-273

DONE

INDEX

INDEX

<xwhome>/prog/au/bin

showpp - AU program started by spdisp (binary file)

SEE ALSOpulsdisp, nmrsim

A-274 Miscellaneous

DONE

INDEX

INDEX

edacb

NAMEedacb - edit the Amplifier Control Board parameters

SYNTAXedacb [<filename>]

DESCRIPTION

The command edacb allows you to edit the ACB parameters and load them to the spectrometer hardware. The ACB parameters define the upper limits above which the power is switched off. These limits are used to protect the probehead in case too high power levels or pulse lengths are used. Normally the default lim-its can be used in which case you do not need to execute edacb. Only for spe-cial probeheads or transmitters, it might be useful to set sharper limits.

At the top of the dialog box, the current probehead (as defined with edhead) is displayed. Below that, the ACB parameters are listed. These are:

• pulse power: pulse power in W(att) or %

• pulse width: pulse length in ms (millisecond) or %

• duty cycle: the (pulse width)/period ratio in %

• reflected power: pulse power not reaching the probe in W(att) or %

where period is defined as the time between the start of two successive pulses. The current values of the ACB parameters are shown for each amplifier (as de-tected by cf). Furthermore, the minimum and maximum allowed values are dis-played for each parameter. The pulse power can be entered with the unit W, without unit (same as W) or with the unit %. The latter is interpreted as is the percentage of the nominal power of the amplifier. The pulse width can be entered with the unit ms, without unit (same as ms) or with the unit %. The latter is in-terpreted as the percentage of the maximum pulse width as specified above the entered value.

Note that the ACB parameters are interdependent. For example, if you decrease the pulse power, you can increase the pulse width or, if you increase the period between the pulses, you can also increase the pulse width.

At the bottom of the dialog box, the following buttons are offered:

Miscellaneous A-275

DONE

INDEX

INDEX

Set parametersSets the current values on the spectrometer hardware. You are first prompted for the NMR Superuser password.

Save as..Saves the ACB values to disk, including minimum and maximum values and probehead identification. You are first prompted for the NMR Superuser password. Then a list of existing filenames and you can select one of them. Alternatively, you can enter a new filename.

Load from..Allows you to read previously saved values from disk. A list of existing files will appear and you can select one of them. If the minimum/maximum values do not match your amplifiers (as detected by cf), or the probehead identifi-cation does not match the current probehead (as defined by edhead) you will get a warning. In that case you are prompted to cancel or continue the loading.

SaveOnly active after the current values have been saved with Save as... Saves the ACB parameters to the filename displayed in the title bar of the dialog box.

AboutDisplays information about the edacb version and software support.

QuitCloses the edacb dialog box discarding all changes.

The command edacb can also be entered with one argument; the name of an ACB parameter file. The values in the file are automatically loaded to the hard-ware. As such, the command edacb <filename> can also be used in auto-mation.

INPUT AND OUTPUT FILES/<xwhome>/conf/instr/<instrum>/acbpar/*

ACB parameters files

SEE ALSOcf

A-276 Miscellaneous

DONE

INDEX

INDEX

crpon, crpoff, crplock, crpobs

NAMEcrpon - switch the cryo preamplifier on for the lock and observe channelcrpoff - switch the cryo preamplifier off for the lock and observe channelcrpobs - switch the cryo preamplifier on for the observe channelcrplock - switch the cryo preamplifier on for the lock channel

DESCRIPTIONThe crp* commands listed above control the internal preamplifier of a cryo-probe. Cryo probeheads operate at a reduced coil and preamplifier temperature which improves the signal to noise with a factor of 4. They are available as Dual or Triple resonance probeheads.

The command crpon switches from the external (HPPR) preamplifier to the in-ternal cryo preamplifier. This happens for both the observe and the lock channel.

The command crpoff switches from the internal cryo preamplifier to the ex-ternal (HPPR) preamplifier. This happens for both the observe and the lock channel.

The command crplock switches from the external (HPPR) preamplifier to the internal cryo preamplifier. This happens for the lock channel only.

The command crpobs switches from the external (HPPR) preamplifier to the internal cryo preamplifier. This happens for the observe channel only.

SEE ALSO

edhead

Miscellaneous A-277

DONE

INDEX

INDEX

getlim1d, getlcosy, getlxhco, getljres, getlinv

NAMEgetlim1d - determine the 1D spectral width according to integral rangesgetlcosy - determine the 2D cosy spectral width according to 1D integral rangesgetlxhco - determine the 2D xhco spectral width according to 1D integral rangesgetljres -determine the 2D jres spectral width according to 1D integral ranges getlinv - determine the 2D invers spectral width according to 1D integral ranges

DESCRIPTION

The getl* commands listed above determine and set the optimum spectral width for the specified experiment types. The optimum spectral width is deter-mined from one or two associated 1D datasets that are defined as the so called second and third dataset (see edc2). Before the actual experiment is performed, the second (and if necessary the third) dataset must be acquired, Fourier trans-formed and baseline corrected. The latter processing step implicitly determines the integral ranges. The getl* commands determine the spectral width such that it includes all integral ranges, in other words, all signals.

getl* commands are typically used in automation. They are called from AU programs like au_getl1d, au_getlcosy, au_getlinv and au_getlxhco. These, in turn are called by ICON-NMR where the preparation and the actual experiment are defined as a so-called ’composite’ 2D experiment (see ICON-NMR Online help for more information).

getlim1d determines the optimum spectral width on a 1D preparation exper-iment and then sets the parameter SW on the current 1D dataset accordingly.

getlcosy determines the optimum spectral width on one 1D preparation ex-periment. Then it sets the F2-SW and F1_SW on the current 2D COSY dataset accordingly.

getlxhco determines the optimum spectral width for F2 and F1 on two differ-ent 1D preparation experiments (typically 1H and X). Then it and sets the F2-SW and F1-SW on the current 2D XH correlation dataset accordingly.

getljres determines the optimum spectral width on one 1D preparation ex-periment. Then it sets F2-SW on the current 2D J-resolved dataset in according-ly.

A-278 Miscellaneous

DONE

INDEX

INDEX

getlinv determines the spectral width on one 1D preparation experiment. Then it sets F2-SW on the current 2D INVERSE dataset accordingly.

Note that F2-SW refers to the acquisition parameter SW in the F2 dimension and F1-SW refers to the same parameter in the F1 dimension.

The first 1D preparation experiment is defined as the so called second dataset. The second 1D preparation experiment is defined as the so called third dataset Both can be defined with the command edc2.

OUTPUT PARAMETERSSW - spectral width in ppm

INPUT FILES<du>/data/<user>/nmr/<name>/<expno>/pdata/<procno>

intrng - integral regionscurdat2 - definition of second and third dataset


acqu - acquisition parametersacqu2 - F1 acquisition parameters of a 2D dataset

USAGE IN AU PROGRAMSGETLIM

executes the command getlim1d

GETLCOSY

GETLXHCO

GETLJRES

GETLINV

A-279

Chapter 14

NMR Suite files

This chapter describes the files which are involved in XWIN-NMR acquisition. For each file, the commands that typically create or modify the file are specified. If no command is specified, the file is delivered with XWIN-NMR and not modified by any command. Furthermore, the commands that typically interpret a file are speci-fied. If no command is specified, the file can usually be read from a UNIX shell or Windows Explorer or is to be used by a external program. Note that the specified commands can be started, manually, from the XWIN-NMR command line or, auto-matically, from an AU program or ICON-NMR. Files that are created by ICON-NMR are not described here but in the ICON-NMR manual. Note that, for each file, only the most important commands that access the file are mentioned here.

For each file, the file type is specified which has one of the following letters:

• a - ascii file. It can be opened by a text editor.

• j - JCAMP-DX file. It can be opened with a text editor and interpreted by any software which supports JCAMP-DX.

• b - binary file. Data file with consecutive 32-bit integer values.

• e - binary executable

• d - directory with files and/or sub directories

• t - Tcl/Tk script

A-280 NMR Suite files

DONE

INDEX

INDEX

1D data files

FileCreated or

modified byaInterpreted

byDescription (file type)

<du>/data/<user>/nmr/<name>/<expno>

fid zg, genfid bc, em, ft 1D raw data (b)

acqu rpar, eda zg acquisition parameters (j)

acqus rpar, zg dpa, lpa acquisition status parameters (j)

audita.txt zg acquisition audit trail (j)

pulse_program

zg precompiled pulse program (j)

format.lpa zg lpa acquisition parameter format (a)

format.temp zg plot, view acquisition parameter format (a)

relations getprosol prosol-acquisition relations (a)

cpdprg1zg (cpd1)zg (cpds1)

CPD program defined by CPDPRG1 (a)

cpdprg2zg (cpd2)zg (cpds2)

CPD program defined by CPDPRG2 (a)

etc.

scon zg copy of the edscon parameters (j)

spnam1 zg (sp1) shaped pulse definition (j)

spnam2 zg (sp2) shaped pulse definition (j)

etc.

fq1list zg (fq1) variable frequency list (j)

fq2list zg (fq2) variable frequency list (j)

etc.

vclist zg (vc) variable counter list (a)

vdlist zg (vd) variable delay list (a)

vplist zg (vp) variable pulse list (a)

vtlist variable temperature list (a)

popt.array popt popt parameter optimization setup (a)

NMR Suite files A-281

DONE

INDEX

INDEXpopt.proto-col

popt poptparameter optimization result (a)

masRateLogmasrmon,

mascontrolMAS spin rate log file (j)

cag_par zg gradient rotation matrices

a. Some files are only created if the corresponding pulse program statement (specified be-tween brackets) is used.

2D data files

FilenameCreated or updated by

Interpreted by

Description (file type)


ser zg, genser xfb, xf2 raw data - series of FIDs (b)

acqu rpar, eda zg F2 acquisition parameters (j)

acqu2 rpar, eda zg F1 acquisition parameters (j)

acqus rpar, zg dpa F2 acquisition status parameters (j)

acqu2s rpar, zg dpa F1 acquisition status parameters (j)

Various lists as specified under 1D data files.

1D data files

FileCreated or

modified byaInterpreted

byDescription (file type)


DONE

INDEX

INDEX

3D data files

FilenameCreated or modified by

Inter-preted by



ser zg tf3 raw data - series of FIDs (b)

acqu rpar, eda zg F3 acquisition parameters (j)



acqus rpar, zg dpa F3 acquisition status parameters (j)



Various lists as specified under 1D data files.

User defined settings

FileCreated or modified by

Interpreted by


<userhome>/.xwinnmr-<hostname>/

resources setreszg, edcpul, edau, plot

XWIN-NMR resource settings (j)

default.por search search default portfolio (a)

autoshim gradshim gradient shimming directory (d)

<xwhome>/prog/curdir/<user>

history hist onhistory of commands and error mes-sages (a)

curdat edc, new edc, new currently displayed dataset (j)

individual_user_note

book.txt

Help ��individualuser...

Help ��individualuser...

individual user notebook (a)


DONE

INDEX

INDEX

AU Programs


Interpreted by Description (file type)

<xwhome>/prog/au/src.exam

* expinstall Bruker AU program sources (a)

<xwhome>/prog/au/bin

*compileall cpluser,edau

xau a User defined AU executables (e)

*compileall cplbruk,edau

xau Bruker AU executables (e)

<xwhome>/prog/include/

aucmd.h edau AU macro definitions (a)

<xwhome>/prog/include/inc

* edau AU macro and inclusion files (a)

<xwhome>/exp/stan/nmr/au

scr expinstall cplbruk, xau Bruker AU sources (d)

scr edau cpluser, xau User defined AU sources (d)

vorspann edau C-languages definition file (a)

makeau edau AU compilation script (a)

<xwhome>/exp/stan/nmr/au/src

* expinstallcompileall cplbruk,edau

Bruker AU sources (a)

* edaucompileall cplbruk,edau

User defined AU sources (a)

a. Note that AU programs can be started by entering xau <name> or simply <name>


DONE

INDEX

INDEX

Documentation files

FilenameInterpreted by


<xwhome>/prog/docu/english

xwinproc/pdf Helpmanuals for acquisition, processing, installation, release letter etc. (d)

avance/pdf Help Avance spectrometer users guide (d)

xwpman/pdf Help XWIN-PLOT manuals (d)

iconman/pdf Help ICON-NMR manuals (d)

NMR Suite executables

FilenameInterpreted by


<xwhome>/prog/cpr

xcpu XWIN-NMR XWIN-NMR graphics program (e)

cpr XWIN-NMR XWIN-NMR command interpreter (e)

<xwhome>/prog/mod

confed cf configuration module (e)

edparproc eda, edp parameter editor module (e)

expinstall expinstall AU and parameter installation module (e)

go zg, go, wobb acquisition module (e)

proc1d em, ft, pk 1D processing module (e)

shimcntl lock, rsh lock and shim module (e)

..

see also Tcl/Tk scripts and AU programs


DONE

INDEX

INDEX

Tcl/Tk scripts

Filename Interpreted by



butselnmr butselnmr Easy interface for selective experiments (t)

buttonnmr buttonnmr Easy interface for standard experiments (t)

config config Spectrometer configuration (t)

edhead edhead Probehead selection (t)

edprosol edprosol Probehead/Solvent dependent parameter setup (t)

glp glp Program Good Laboratory Practice (t)

gradshim gradshim Gradient shimming (t)

iconnmr gradshim ICON-NMR interface (t)

mascontrol mascontrol MAS control and monitor (t)

masrmon masrmon MAS monitor (t)

popt popt Multiple parameter optimization (t)

smail smail Data transfer by Email (t)

temon temon Temperature monitor (t)


DONE

INDEX

INDEX

Spectrometer configuration files


Interpreted by



curinst cf cf spectrometer name (a)

patchlev XWIN-NMR patchlevel (a)

hardware.examcf

makelistexample hardware list containing all possible hardware devices (a)

nmr_user_notebook.txt

Helpnotebook for all NMR users (a)

system_notebook.txt

Helpnotebook for system administrator (a)

probehead edheadlock,edlock, getprosol edprosol

current probe definition (a)

probeheads edhead edhead probe parameter files (d)


2Hlock edlock lock, lopo 2H lock table (a)

bacs_params cfbacs, cf sample changer information (a)

uxnmr.info cf spectrometer configuration over-view (a)

cortab cortab zgamplifier power and phase correc-tion tables (d)

uxnmr.par cf spectrometer configuration (j)

nuclei cf, ednuc edasp nuclei table (a)

scon edscon zg spectrometer fine tuning settings (j)

specpar edsp, edasp zg routing information

hardware_ list cf list of hardware components that are not automatically detected (a)

mas_params cfmas masi, mase information about the MAS unit (a)


DONE

INDEX

INDEXprosol edprosol getprosol

probe/solvent dependent parameter files (d)

autoshim gradshim gradshim gradient shimming files (d)

bbis_bla1 cf ii, zg linear amplifier information (a)

bbis_bla2 cf ii, zg linear amplifier information (a)

etc.

bbis_fcu1 cf ii, zg fcu1 information (a)

bbis_fcu2 cf ii, zg fcu2 information (a)

etc.

bbis_rcu cf ii, zg rcu information (a)

bbis_tcu cf ii, zg tcu information (a)

bsmsdisp. calibr bsmsdisp BSMS display calibration (a)

<xwhome>/conf/instr/<curinst>/rs232_device

acb cf acbdisp ACB rs232 channel + settings (a)

bacs cfbacs, cf sample changer rs232 channel (a)

bsms cf lock, rsh BSMS rs232 channel + settings (a)

lock cf lockdisp lock display rs232 channel (a)

preamp1 cf zg, ii, rga first HPPR rs232 channel (a)

preamp2 cf zg, ii, rga second HPPR rs232 channel (a)

..

preemp cf zg preemphasis channel + settings (a)

rx22 cf zg RX22 receiver channel + settings (a)

temp cfte, cf edte, teset temperature unit rs232 channel (a)

<xwhome>/conf/instr/servtool a

acbtool NMR-CHECK ACB service tool (d)



Interpreted by



DONE

INDEX

INDEXbsmstool NMR-CHECK BSMS service tool (d)

gradtool Gradient service tool (d)

hpcutool HPCU service tool (d)

hpprool NMR-CHECK HPPR preamplifier service tool (d)

rx22tool NMR-CHECK Rx22 receiver service tool (d)

Unitool Generic service tool for AQS and HPPR II (d)

a. Service tools can be executed from the Windows Command prompt (or UNIX shell) or fromNMR-CHECK.



Interpreted by



DONE

INDEX

INDEX

Format files

FilenameCreated or modi-fied by

Interpreted by


<xwhome>/exp/stan/nmr/form/

acb.e edacb acquisition control board parameters (a)

acqu.e cf eda acquisition parameters (a)

acqu.e.D cf acquisition parameters for Avance (a)

acqu.e.X cfacquisition parameters for AMX with SCM (a)

acqu.e.R cfacquisition parameters for ARX with SCM (a)

acqu.e.X.B cfacquisition parameters for AMX with BSMS (a)

acqu.e.R.B cfacquisition parameters for ARX with BSMS (a)

curd.e edc current data path parameters (a)

curd2.e edc2 second data path parameters (a)

dosy.e eddosy dosy parameter (a)

edp3.e edp3 F3 processing parameters in 3D (a)

edp2.e edp2 F2 processing parameters in 2D/3D (a)

edp1.e edp1 F1 processing parameters in 2D/3D (a)

hpcu.e cf edhpcu acquisition + HPCU parameters (a)

hpcu.e.D cf acqu. + HPCU parameters for Avance (a)

hpcu.e.X cfacqu. + HPCU parameters for AMX - SCM (a)

hpcu.e.X.B cfacqu. + HPCU parameters for AMX - BSMS (a)

outd.e edo output parameters (a)

proc.e edp processing parameters in 1D/2D/3D (a)

preemp.e edpre preemphasis parameters (a)


DONE

INDEX

INDEXspec.e edsp, edasp routing format file on AMX/ARX

scon.e cf edsconspectrometer constants for your spectrometer (a)

scon.e.A cf spectrometer constants for Avance-AQS (a)

scon.e.D cf spectrometer constants for Avance-AQS (a)

used_from.e

edc2 used _from

source 2D data path parameters (a)

maxent1d.e maxed 1D MAXENT parameters (a)



t1par t1/t2 T1/T2 relaxation format files (d)

plot edx 1D plot parameter format files (d)

plot2 edx 2D plot parameter format files (d)

plotw edgw stack plot parameter format files (d)

plotx edgx extended plot parameter format files (d)

acqu.ldpa, lpa, plot

acqu. status format files for the first dimen-sion of 1D, 2D or 3D data (d)

acqu2.ldpa, lpa, plot

acqu. status format files for the second dimension of 2D or 3D data (d)

acqu3.ldpa, lpa, plot

acqu. status format files for the third dimen-sion of 3D data (d)

curd.ldpc, lpc, plot

current dataset status format files (d)

outd.ldpo, lpo, plot

output status parameters (d)

plot.ldpo, lpo, plot

1D plot status format files (d)

Format files


Interpreted by



DONE

INDEX

INDEX

plot2.ldpo, lpo, plot

2D plot status format files (d)

proc.ldpp, lpp, plot

processing status format files for the first dimension of 1D, 2D or 3D data (d)

proc2.ldpp, lpp, plot

processing status format files for the second dimension of 2D or 3D data (d)

proc3.ldpp, lpp, plot

processing status format files for the third dimension 3D data (d)

<xwhome>/exp/stan/nmr/form/acqu.l

formased asedacquisition parameters used in pulse program (a)

normdp dpa acquisition status parameters to be viewed (a)

normlp lpa acquisition status parameters to be printed (a)

normpl plot, view acquisition status parameters to be plotted (a)

normdp.D cf acquisition status parameters for Avance (a)

normdp.R cfacqu. status parameters for ARX with SCM (a)

normdp.R.B cfacqu. status parameters for ARX with BSMS (a)

normdp.X cfacqu. status parameters for AMX with SCM (a)

normdp.X.B cfacqu. status parameters for AMX with BSMS (a)

hpcudp dpa as normdp + HPCU parameters (a)

hpculp lpa as normlp + HPCU parameters (a)

hpcupl plot, view as normlp + HPCU parameters (a)

Format files


Interpreted by


A-293

Chapter 15

Bruker addresses

GermanyBruker BioSpin GmbHSilberstreifenD-76287 RheinstettenTel: (++49) (721) 51 61 0Fax: (++49) (721) 51 71 01

Bruker BioSpin Software DepartmentSilberstreifenD-76287 RheinstettenTel: (++49) (721) 5161 440Fax: (++49) (721) 5161 480

http://www.bruker-biospin.de

ftp server: ftp.bruker.de

Email: [email protected] (sales) [email protected] (service) [email protected] (application) [email protected] (software) [email protected] (licenses)

http://www.bruker-biospin.de

ftp.bruker.de

A-294 Bruker addresses

DONE

INDEX

INDEX

USABruker BioSpin Corporation15 Fortune Drive Manning RoadBillerica, MA. 01821-3991

Tel: (++1)(978) 667 9580 195 (center) (++1)(978) 667 9580 444 (application)Fax: (++1)(978) 667 6168 (center) (++1)(978) 667 2955 (application)

http://www.bruker-biospin.comftp server: ftp.bruker.com

Email: [email protected] [email protected] [email protected]

SwitzerlandBruker BioSpin AGIndustriestraße 26CH-8117 Fällanden

Tel: (++41)(1) 8 25 91 11Fax: (++41)(1) 8 25 96 96

web server: www.bruker.chE-Mail: [email protected]

[email protected]

FranceBruker BioSpin S.A.34, rue de l’industrieF-67166 Wissembourg/Cedex

Tel: (++33)(3) 88 73 68 00Fax: (++33)(3) 88 73 68 79

E-Mail: [email protected] (customer support)

EnglandBruker BioSpin LTD.Banner lane

http://www.bruker-biospin.com

ftp://ftp.bruker.com

www.bruker.ch

Bruker addresses A-295

DONE

INDEX

INDEX

Coventry CV4 9GHTel: (++44)(2476) 855200Fax: (++44)(2476) 465317

Email:[email protected] [email protected]

Our webpage

http://www.bruker-biospin.de/analytic/nmr-dep/about/offices/contact.htm

provides contact addresses of our facilities and offices worldwide

http://www.bruker-biospin.de/analytic/nmr-dep/about/offices/contact.htm

Command Index

Command - Index A-xx: Acquisition Reference Manual P-xx: Processing Reference Manual

Aabs P-48abs1 P-136abs2 P-138absd P-48absd1 P-136absd2 P-138absf P-48absot1 P-140absot2 P-142abst1 P-140abst2 P-142acqu A-192add P-51add2d P-144addc P-53addfid P-51and P-54apk P-56apk0 P-56apk1 P-56apkf P-56apks P-56as A-150ased A-150atma A-134atmm A-136auditcheck P-500autoplot P-298autoshim A-120

Bbc P-58bcm P-60bcm1 P-146bcm2 P-146browse P-384butselnmr A-193buttonnmr A-196Ccf A-62cfbacs A-67cfbpsu A-68cfmas A-240cfte A-69compileall A-70, P-416config A-71conv P-478convdta P-484convsys P-483cortab A-73cplbruk A-81, P-417cpluser A-81, P-417crplock A-276crpobs A-276crpoff A-276crpon A-276ct1 P-351ct2 P-354Ddat1 P-357del P-385

Command Index

DONE

INDEX

INDEX

del2d P-389dela P-385delau A-260, P-419deldat P-385delf P-389delgp A-260, P-419deli P-389dellist A-262, P-421delmac A-260, P-419delmisc P-423delp P-385delpar A-260, P-419delpul A-260, P-419dels P-389delser P-389delsh A-260, P-419dir P-392dir2d P-395dira P-392dirdat P-392dirf P-395diro P-397dirp P-392dirpar P-424dirs P-395dirser P-395div P-62dosy2d P-148dosy3d P-252dp P-425dpa A-152, P-426dpc P-428dpg P-429dpgx P-430dpo P-431

dpp P-432dt P-64duadd P-65Eed4ph A-243eda A-154edacb A-274edasp A-156edau A-172, P-434edc P-399edc2 P-401edcgp A-174, P-436edcpd A-176, P-438edcpul A-177, P-439eddosy P-441edg P-300edgp A-179, P-443edgw P-300edgx P-300edhead A-138edhpcu A-242edinfo P-302edlev P-304edlist A-180, P-444edlock A-104edmac P-446edmisc P-448ednuc A-83edo P-402edp P-450edp1 P-453edp2 P-453edp3 P-453edprosol A-85edpul A-188, P-454

Command Index

DONE

INDEX

INDEX

edscon A-89edsolv A-93edsp A-95edt1 P-359edte A-228edtg A-229edtune A-121ef P-67efp P-67ej A-142elim P-360em P-69expinstall A-97, P-456expt A-199Ff1disco P-149f1projn P-151f1projp P-151f1sum P-154f2disco P-149f2projn P-151f2projp P-151f2sum P-154filt P-72flplot P-306fmc P-71follow P-502fp P-74fromjdx P-486ft P-75Ggdcheck P-503gdcon P-79genfid P-81genser P-156

gethpcu A-257getlcosy A-277getlim1d A-277getlinv A-277getljres A-277getlxhco A-277getprosol A-160gf P-83gfp P-83gm P-85go A-200gs A-202Hhalt A-204hist P-504hoff P-505hon P-505ht P-87Iiconnmr A-206ift P-89ii A-207ij A-142int2d P-307int2dref P-307Jjconv P-492Kkill P-506Lldcon P-90levcalc P-309lfilter A-108lgain A-108li P-311

Command Index

DONE

INDEX

INDEX

limits2d P-313lipp P-314lippf P-314lock A-110lockdisp A-114lopo A-116lopoi A-116lp P-316lpa P-317lpc P-318lpg P-319lpgx P-320lpo P-321lpp P-322lppl P-323ls P-92lsta P-364lstp P-362ltime A-108Mmas A-245mascontrol A-249mase A-252masg A-252mash A-252masi A-252masr A-252masrmon A-255mc P-94mdcon P-95mul P-97mulc P-99Nnm P-100nxtp P-366

Oor P-101Ppaste P-404pd P-368pd0 P-368pft2 P-371pk P-103plot P-324plotreg P-327plots P-324plotw P-324plotx P-324popt A-208pp P-328pp2d P-333pp2dmi P-333pph P-328ppj P-328ppp P-328pps P-328ppt1 P-373proj P-158ps P-105ptilt P-160ptilt1 P-162pulsdisp A-268Qqsin P-106qsinc P-108Rr12 P-285r12d P-291r12p P-294r13 P-287

Command Index

DONE

INDEX

INDEX

r13d P-292r13p P-295r23 P-289r23d P-293r23p P-296rackpow A-257re P-406ren P-408renau A-264, P-461rengp A-265, P-462renlist A-266, P-465renlut A-265, P-462renmac A-265, P-462reno P-408renpar A-264, P-461renpul A-265, P-462rep P-406resume A-212rev1 P-164rev2 P-164rga A-213rhnp P-165rhpp P-165rlut P-335rmisc P-463rmplot P-336ro A-143rpar A-163, P-466rs P-110rsc P-168rser P-173rser2d P-176rsh A-122rspc P-375rsr P-178

rstp P-376rv P-112rvnp P-165rvpp P-165Ssab P-113search P-409setdef P-507sethpcu A-257setres P-508setsh A-124setti P-337show P-509simfit P-377sinc P-115sinm P-117sino P-338spdisp A-272sref P-341status P-510stop A-214sub1 P-181sub1d1 P-181sub1d2 P-183sub2 P-183suspend A-215sym P-185syma P-187symj P-189Ttabs1 P-257tabs2 P-255tabs3 P-253te2get A-230te2ready A-234

Command Index

DONE

INDEX

INDEX

te2set A-236teget A-230temon A-231tepar A-233teready A-234teset A-236tf1 P-271tf1p P-280tf2 P-266tf2p P-278tf3 P-259tf3p P-276tht1 P-284tht2 P-283tht3 P-282tilt P-191tm P-119tojdx P-489tr A-216traf P-126trafs P-126trf P-121trfp P-121tune A-125Uuwm P-127Vvconv P-495view P-344viewmg P-344vieww P-344viewx P-344vish A-130Wwmisc P-470

wobb A-145wpar A-167, P-472wra P-411wrd P-411wrp P-411wrpa P-411wsc P-193wser P-196wserp P-199wsh A-131wsr P-202Xxau A-217, P-474xaua A-217, P-474xaup A-217, P-474xf1 P-205xf1m P-208xf1p P-210xf1ps P-212xf2 P-214xf2m P-208xf2p P-218xf2ps P-212xfb P-220xfbm P-208xfbp P-233xfbps P-212xhelp P-511xht1 P-235xht2 P-236xif1 P-237xif2 P-237xmac P-476xor P-129xtrf P-239

Command Index

DONE

INDEX

INDEX

xtrf2 P-239xtrfp P-243xtrfp1 P-243xtrfp2 P-243xwinplot P-345xwp_lp P-346xwp_pp P-348Zzert1 P-246zert2 P-248zf P-131zg A-220zp P-133

Index - i

Index

Numerics

2D lookup tables A-2654-phase modulator A-90, A-243

A

abs command A-36, A-53, A-197ACB parameters A-274ACB service tool A-287accumulation of the FID A-192acqu command A-221acquisition

dimension A-44, A-46interface A-193, A-196menu A-192, A-196, A-202mode A-12, A-44, A-52order A-53parameters A-7, A-8, A-9, A-10, A-11, A-154,

A-163, A-164, A-165, A-167, A-192,A-202, A-204, A-208, A-280, A-281,A-282, A-289

status parameters A-7, A-9, A-52, A-152, A-280, A-281, A-282, A-291

time A-11, A-45, A-150air flow A-142, A-247, A-249, A-252, A-253amplifier

correction table A-73linearization A-73routing A-32, A-34, A-156, A-158

amplitude list A-181, A-183Amplitude Setting Unit A-73AMX spectrometer A-17, A-25, A-98, A-100, A-111,

A-181analog filter A-17, A-23apk command A-53, A-197, A-223ARX spectrometer A-98, A-101, A-111as command A-150

ased command A-150, A-154, A-220ASU

blanking A-89correction A-73linearization A-76

ATM probehead A-134, A-136, A-148, A-220atma command A-51, A-134, A-136, A-220atmm command A-136attenuator A-73AU program

binaries A-70, A-81, A-97, A-173, A-283Bruker defined A-70, A-81, A-97, A-172compilation A-70, A-81, A-172, A-217creation A-172deletion A-260edit A-172execution A-217files A-283for acquisition A-12, A-192, A-218for processing A-218installation A-97kill A-218macro A-4, A-5rename A-264sources A-70, A-81, A-173, A-283user defined A-81, A-97, A-172

au_zg AU program A-13, A-192auto lock-in A-110, A-111, A-193, A-196autolock key A-54, A-108, A-112, A-116automatic

receiver gain optimization A-213shimming A-121, A-125, A-128, A-193, A-196tuning and matching A-134

automation with Icon-nmr A-5, A-43, A-67, A-87, A-106, A-140, A-206, A-218, A-277

autoshim A-120Avance spectrometer A-5, A-31, A-98, A-100, A-

111, A-181, A-284

Index - ii

DONE

INDEX

INDEX

B

basic frequency A-13, A-32, A-34, A-57, A-59, A-83,A-104, A-147, A-156

BPSU unit A-68, A-71Bruker

AU programs A-70, A-81, A-97, A-172, A-200,A-264, A-283

CPD programs A-15, A-176gradient files A-24gradient programs A-179parameter sets A-14, A-34, A-98, A-104, A-158,

A-164, A-168, A-218, A-260pulse programs A-15, A-23, A-30, A-36, A-40,

A-177, A-188, A-215, A-265shape files A-42solvent list A-93spectrometers A-17, A-227

Bruker addresses A-293BSMS

display A-104, A-122, A-143, A-287keyboard A-8, A-54, A-58, A-104, A-106, A-

108, A-111, A-112, A-114, A-116, A-119, A-122, A-128, A-142, A-143, A-146

lock unit A-111rs232 channel A-65service tool A-288unit A-54, A-103, A-105, A-111, A-112, A-126,

A-143bsmsdisp command A-104, A-122, A-143butselau AU program A-195butselnmr A-193buttonau AU program A-198buttonnmr command A-39, A-196, A-223

C

calibration A-59, A-105carrier frequency A-34, A-35, A-41, A-99, A-100cf command A-13, A-32, A-62, A-97cfbacs command A-65, A-67cfbpsu command A-68cfmas command A-240, A-249, A-253cfte command A-68, A-69chemical shift A-35, A-59, A-105, A-111communication problems A-62

compilation of AU programs A-81, A-97, A-172, A-217

compileall command A-70, A-97, A-217composite experiments A-277composite pulse decoupling A-14, A-176config command A-32, A-62, A-71configuration

commands A-61files A-286of the BPSU unit A-68of the MAS unit A-240of the sample changer A-67of the spectrometer A-62of the temperature unit A-69of XWIN-NMR A-222suite A-62, A-71

contour levels A-163, A-164, A-165, A-166, A-168,A-169

conventions in this manual A-3Cortab

experiment A-73, A-77linearization A-73program A-73verification A-73

cortab command A-73counter list A-181CPD

command A-37power level A-161programs A-14, A-38, A-97, A-100, A-176, A-

187pulse length A-37, A-151, A-161

cplbruk command A-81, A-97, A-217, A-260cpluser command A-81, A-217crplock command A-276crpobs command A-276crpoff command A-276crpon command A-276cryo preamplifier A-276

D

data path parameters A-289dataset list A-19, A-181decimation factor A-16, A-21, A-53define statement A-50, A-98

Index - iii

DONE

INDEX

INDEX

delau command A-260delay list A-181delete

AU programs A-260gradient programs A-260macros A-260parameter sets A-260pulse programs A-260shim files A-260various lists A-262

delgp command A-260dellist command A-262delmac command A-260delpar command A-260delpul command A-260delsh command A-260demand

spin rate A-143, A-240, A-246, A-249, A-252temperature A-46, A-230, A-234, A-236, A-245

deuterium A-104digital

digitizer resolution A-15, A-18filtering A-5, A-15, A-16, A-17, A-20, A-21, A-

53lock A-103quadrature detection A-12, A-18

digitizermode A-17resolution A-15, A-18start A-16type A-11, A-17, A-18, A-23, A-100

dimension2D direct A-4, A-9, A-322D indirect A-4, A-9, A-31, A-44, A-463D direct A-93D indirect A-5, A-9

dimensionality of data A-36, A-164DNA/RNA experiments A-160dpa command A-7, A-8, A-52, A-152DQD

device A-12mode A-18

DSP firmware A-54dummy scans A-18, A-150, A-220, A-221, A-269duty cycle A-274

dwell time A-17, A-20, A-43, A-150

E

ed4ph command A-243eda command A-7, A-8, A-10, A-11, A-161, A-164,

A-168edacb command A-274edasp command A-13, A-21, A-25, A-31, A-32, A-

34, A-38, A-57, A-220edau command A-5, A-38, A-97, A-172, A-217edc command A-168, A-193, A-196, A-220edcgp command A-174edcpd command A-15, A-176, A-187edcpul command A-39, A-177, A-179edg command A-164, A-168edgp command A-179, A-187edgx command A-164edhead command A-40, A-56, A-85, A-104, A-138,

A-220edhpcu command A-242edlev command A-164edlist command A-19, A-23, A-47, A-48, A-49, A-50,

A-180edlock command A-8, A-29, A-87, A-104, A-108, A-

110, A-116edmac command A-5, A-187ednuc command A-13, A-63, A-83edo command A-105, A-164, A-168edp command A-154, A-164, A-168edprosol command A-8, A-39, A-43, A-85, A-125, A-

161, A-220edpul command A-36, A-187, A-188edscon command A-16, A-89, A-224edsolv command A-93edsp command A-95, A-156edte command A-228, A-233edtg command A-229edtune command A-121, A-125ef command A-197efp command A-194ej command A-142eject

air time A-240, A-247mechanism A-240the sample A-247, A-249, A-253

Index - iv

DONE

INDEX

INDEX

the spinner A-252em command A-53, A-194, A-223eurotherm temperature unit A-227experiment time A-31, A-197, A-199expinstall command A-17, A-40, A-70, A-81, A-96,

A-97, A-98, A-164, A-172, A-188expt command A-31, A-192, A-199

F

FIDarea A-127display A-12, A-34, A-41, A-202, A-203envelope A-125number A-36resolution A-21, A-46signal A-40

field value A-104, A-105, A-114follow command A-218font conventions A-3format files A-289frequency

list A-23, A-181, A-182, A-225, A-280unit A-268

ft command A-36, A-53, A-194, A-223

G

gethpcu command A-257getlcosy command A-277getlim1d command A-277getlinv command A-277getljres command A-277getprosol command A-8, A-39, A-43, A-87, A-160,

A-193, A-197, A-220getxhco command A-277go command A-11, A-200, A-222gpro command A-160gradient

experiment A-198file A-24, A-25, A-97, A-98parameter table A-23parameters A-24, A-25program A-25, A-100, A-174, A-179, A-187, A-

260, A-265pulse length A-161recovery delay A-161

service tool A-288shaped A-24shimming A-25, A-220, A-282, A-287static A-24strength A-24

gradshim command A-220group delay A-5, A-53, A-54gs command A-11, A-12, A-34, A-41, A-192, A-202,

A-214

H

halt command A-31, A-135, A-200, A-204, A-212,A-214, A-215, A-222

hard pulse A-86, A-87, A-161hardware list A-64, A-67, A-240, A-286hardware resolution A-15, A-18high power

accessory A-38amplifier A-25, A-33, A-157cabinet A-257output A-33, A-157preamplifier A-25routing A-58, A-100, A-159tube transmitter A-242, A-257

holder position A-56homodecoupling

duty cycle A-25experiment A-17power level A-161

homogeneity of the magnetic field A-114, A-125hostname A-62hosts file A-62, A-64HPCU

parameters A-242service tool A-288unit A-257

HPPR preamplifier A-25, A-147, A-276service tool A-288

I

iconnmr command A-206ii command A-11, A-207ij command A-142impedance

of a probehead A-145, A-146, A-147

Index - v

DONE

INDEX

INDEX

input parameters A-8insert

airtime A-240, A-246, A-247, A-249, A-252the sample A-142, A-246, A-247the spinner A-247, A-249, A-252

integral ranges A-187, A-277interface

of the spectrometer A-207irradiation frequency A-23, A-32, A-34, A-35, A-41,

A-57, A-59, A-99, A-100, A-111, A-151,A-156, A-182, A-202

irradiation frequency offset A-35, A-57, A-59, A-105,A-182, A-202

K

kill command A-135, A-204, A-214, A-218, A-222

L

LC-NMR A-68, A-71, A-160lfilter command A-106, A-108lgain command A-55, A-106, A-108liprosol command A-87lock

channel A-276display A-106, A-114display file A-115frequency A-104, A-114gain A-110irradiation frequency A-59level A-126, A-127nucleus A-28, A-104, A-114parameters A-7, A-29, A-58, A-71, A-104, A-

110, A-116phase A-59, A-105, A-106, A-110, A-114, A-

116, A-128power A-55, A-59, A-104, A-105, A-106, A-

110, A-116regulator cut-off frequency A-55, A-59, A-104regulator filter A-108regulator gain A-54, A-59, A-104, A-108regulator time A-55, A-59, A-104, A-108shift A-55signal A-105, A-106, A-110, A-112, A-114, A-

116status A-56

sweep A-106table A-104

lock command A-8, A-29, A-43, A-58, A-105, A-108, A-110, A-116, A-193, A-196, A-220

lockdisp command A-106, A-112, A-114, A-220lock-in procedure A-58, A-110, A-111, A-116logical frequency channel A-21, A-32, A-58, A-86,

A-100, A-156, A-159loop counter A-27loop filter A-55, A-59, A-104, A-106, A-108, A-111,

A-116loop gain A-54, A-59, A-106, A-108, A-111, A-116loop time A-55, A-59, A-104, A-106, A-108, A-111,

A-116loopadj AU program A-106, A-108lopo command A-8, A-29, A-43, A-58, A-105, A-

112, A-116lopoi command A-29, A-116ltime command A-106, A-108

M

macrosin AU programs A-5, A-283in XWIN-NMR A-5, A-187, A-260, A-262, A-

265magic angle A-239, A-249, A-252magnet

air flow A-142strength A-62type A-67, A-245

MAScommands A-253control A-29, A-245, A-249, A-252log file A-250manual A-253monitor A-55, A-255parameters A-240, A-245pneumatic unit A-71, A-240, A-245, A-246, A-

247, A-249, A-252, A-286spin rate A-29, A-55, A-249, A-253spin rate list A-181, A-187

mas command A-29, A-245, A-249, A-252mascontrol command A-252mase command A-252masg command A-252

Index - vi

DONE

INDEX

INDEX

mash command A-252masi command A-252masr command A-29, A-55, A-252masrmon command A-55, A-249, A-255matching knob A-146, A-147matching the probehead A-51, A-134, A-135, A-136,

A-145, A-192, A-193, A-196mc command A-46micro imaging A-101mixed solvents A-111mixing time A-86multiefp AU program A-194multimas AU program A-186multizg AU program A-223

N

new dataset A-168, A-193, A-196, A-220NMR Superuser A-13, A-62, A-97, A-153, A-155, A-

172nuclei

list A-34, A-83selection A-156table A-13, A-63, A-65, A-83, A-286

O

O1 spikes A-12observe nucleus A-59, A-105optimization

criterion A-208of acquisition parameters A-202, A-208of the lock parameters A-110of the receiver gain A-213protocol of popt A-208

output device parameters A-163, A-164, A-165, A-168

output parameters A-7, A-8overflow A-18, A-35, A-213oversampling A-16, A-17, A-18, A-20, A-23, A-53

dwell time A-17, A-20

P

parametereditor A-8, A-10optimization A-202, A-208sets A-97, A-98, A-163, A-167, A-168, A-218,

A-260, A-264types A-163, A-164, A-167, A-168, A-260value types A-10

paropt AU program A-210paroptlin AU program A-210paroptlog AU program A-210parray AU program A-210phase

alignment A-42, A-43, A-86correction factor A-37correction of a pulse A-37correction of the receiver A-37correction of the spectrum A-16, A-92cycle A-19, A-37, A-200, A-204, A-222list A-202of a pulse A-268of the lock signal A-59, A-105, A-106, A-111,

A-114, A-116, A-128of the receiver A-16, A-91, A-268program A-36values of a shaped pulse A-185

phtran AU program A-37pk command A-194plot

parameters A-7, A-163, A-164, A-165, A-168title A-163, A-164, A-165, A-168

plot command A-194, A-197popt command A-208portfolio A-282power

level A-8, A-38, A-42, A-43, A-86, A-87, A-151, A-161, A-202, A-268, A-269

list A-183mode A-38

preamplifierblanking A-89gain A-39modules A-25, A-33, A-38, A-58, A-96, A-100,

A-157, A-158, A-159of a cryoprobe A-276of an MSL A-39routing A-32, A-33, A-58, A-96, A-99, A-156,

A-157, A-158, A-159switching A-16, A-91tuning and matching A-146

Index - vii

DONE

INDEX

INDEX

preferred output for 19F A-33, A-58, A-96, A-99, A-157, A-158, A-159

preferred preamplifier A-33, A-58, A-96, A-99, A-157, A-158, A-159

pre-scandelay A-15, A-91, A-150subdelays A-16, A-91

probehead A-40, A-104acquisition parameter A-56ATM A-134, A-136broadband A-136, A-147commands A-133cryo A-276current A-104, A-138, A-139, A-220dependent lock parameters A-87dependent parameters A-8, A-43, A-59, A-85,

A-160, A-197, A-220dependent tunefile A-87impedance A-145name A-138parameter editor A-138parameters A-138, A-139resonance circuit A-145resonance frequency A-136, A-145, A-147table A-71, A-138tunefile A-193tuning and matching A-51, A-134, A-136, A-

145, A-193, A-196, A-220type A-245, A-249, A-252

processingcommands A-3, A-7, A-36, A-46, A-52, A-53,

A-54, A-223menu A-192parameters A-7, A-163, A-164, A-165, A-168

prosol command A-87prosol parameters A-7, A-8, A-39, A-85, A-160protein experiments A-160pulsdisp command A-11, A-268pulse channels A-268pulse length

CPD A-37, A-151, A-161decrement A-26display A-271increment A-26of a 180 degree pulse A-161

of a 90 degree pulse A-86, A-145, A-161of a gradient pulse A-161of a hard pulse A-86of a soft pulse A-86parameter A-35reset A-26

pulse list A-181pulse program

Bruker defined A-177, A-188compilation A-220constants A-13creation A-177, A-188current A-177define statements A-98deletion A-260display A-268edit A-177, A-188for AMX A-100for wobble A-135installation A-97label A-27, A-30, A-49, A-183rename A-265timing A-268user defined A-177, A-188

pulsesort AU program A-160

Q

QNP probe A-40qnpset AU program A-40quad images A-12quadrature detection A-12

R

rackpow command A-257raw data A-5, A-7, A-9, A-30, A-36, A-45, A-152, A-

164, A-192, A-197, A-200, A-204, A-222,A-224, A-280, A-281

receiverchannel A-40control A-268gain A-40, A-150, A-202, A-203gain optimization A-213gate A-16, A-91output A-41phase A-16, A-37, A-91, A-268

Index - viii

DONE

INDEX

INDEX

rs232 channel A-66, A-287service tool A-288status A-268

recycle delay A-19, A-212, A-221reference

50 ohm resistor A-145frequency A-40, A-100number A-93, A-138peak A-98phase A-202shift A-59, A-105signal A-59, A-105substance A-13, A-111

referencing the spectrum A-104relations

file A-87, A-160, A-280prosol-acquisition A-87, A-160, A-280

relaxation delay A-151rename

2D lookup tables A-265AU programs A-264gradient programs A-265lists A-266macros A-265parameter sets A-264pulse programs A-265

renau command A-264rengp command A-265renlist command A-266renlut command A-265renmac command A-265renpar command A-264renpul command A-265resonance circuit A-145, A-147resonance frequency

of a probehead A-136, A-145, A-146, A-147resume command A-11, A-200, A-212rga command A-11, A-213ro command A-41, A-67, A-143ROESY experiment A-86, A-161rotation of the sample A-40, A-67, A-126, A-134, A-

143, A-144, A-146, A-249rotor material A-245routing

parameters A-34, A-96, A-158

table A-13, A-32, A-57, A-156, A-157rpar command A-17, A-34, A-36, A-40, A-163, A-

167, A-168, A-193, A-196, A-220rsh command A-122, A-128, A-220RX22

rs232 channel A-66, A-287service tool A-288

RX22 receiver A-16, A-91

S

samplechanger A-64, A-67, A-71depth A-139diameter A-138, A-139, A-240, A-245eject A-142, A-247insert A-142, A-246, A-247position A-142rotation A-67, A-126, A-134, A-143, A-146, A-

249rotation frequency A-40, A-144solvent A-42, A-59temperature A-19, A-221, A-230, A-234, A-236transfer tube A-247, A-249

saturation of the lock signal A-106scaling region file A-98, A-187SCM unit A-111SE451 receiver A-41sensitivity of GS sliders A-203sequential mode A-12, A-18serial port A-63sethpcu command A-257setres command A-173, A-223setsh command A-124setti command A-164SGU verification A-75shape files A-42, A-86, A-98, A-101Shape Tool A-25, A-42shaped gradient

file name A-225shaped pulse

file name A-225, A-280frequency offset A-99in CPD programs A-38list A-181, A-185parameters A-42

Index - ix

DONE

INDEX

INDEX

power A-38shim

commands A-119, A-127definition file A-125file A-122, A-127, A-130, A-131, A-260increment A-127set A-119, A-122unit A-122, A-124, A-127, A-128, A-130value A-122, A-124, A-131, A-220

shimmingautomatically A-125, A-193, A-196manually A-122, A-124on the FID A-125on the lock level A-126on the lock signal A-114using simplex A-127

simplex algorithm A-127simplex AU program A-128simulation pulse sequence A-268simultaneous mode A-12single channel detection A-12sliders

on a probehead A-136, A-147smilies A-53soft pulse A-86, A-87solid state A-33, A-101, A-157, A-240, A-243solvent

acquisition parameter A-42dependent lock parameters A-59, A-87, A-111dependent parameters A-8, A-85, A-160, A-193,

A-197, A-220, A-287list A-93, A-104, A-110table A-71, A-93

solvloop command A-87spdisp command A-272spectral width

acquisition parameter A-43adjustment A-20in 2D data A-26, A-30maximum A-44optimization A-277parameter A-43, A-44

spectrometercommunication problems A-62components A-64

configuration A-61, A-62, A-71, A-96, A-286constants A-89frequency A-98, A-104hardware A-63installation A-64interface A-207internal CPU A-62name A-62, A-63, A-286routing A-32, A-34, A-57, A-95, A-156, A-158type A-62, A-97, A-98

spectrumdisplay A-34, A-41edges A-53noise A-200phase correction A-16, A-37, A-92referencing A-58resolution A-45

spin rate A-29, A-55, A-126, A-143, A-240, A-245,A-249, A-250, A-252, A-255

spinlock tolerance A-240sref command A-29, A-43, A-59, A-105stator of an MAS probe A-240, A-247, A-249, A-252status of raw the data A-152status of the raw data A-7, A-9stdisp command A-25, A-42steady state conditions A-19, A-221stop command A-135, A-147, A-200, A-204, A-212,

A-214, A-215, A-222suspend command A-200, A-212, A-215Switchbox A-33, A-38, A-45, A-58, A-96, A-157, A-

159

T

T1 relaxation A-19, A-221te2get command A-230te2ready command A-234te2set command A-236teget command A-230temon command A-231temperature

acquisition parameter A-46commands A-227list A-50, A-181, A-184, A-280maximum A-231minimum A-231

monitor A-231of the inlet capillary A-234of the inlet cappilary A-230of the probe preamplifier A-276of the probehead coil A-276of the second regulator A-230, A-234, A-236parameter set A-233parameters A-228, A-229stabilization A-19, A-221, A-234unit A-46, A-185, A-227, A-228, A-229, A-230,

A-233, A-236unit configuration A-69, A-71unit rs232 channel A-66, A-287

temporary parameters A-8tepar command A-233teready command A-234teset command A-46, A-234, A-236tf3 command A-53time domain A-45, A-150TMS A-111TOCSY experiment A-30, A-86, A-161tomography A-101tr command A-216, A-221transfer data to disk A-216transmitter

blanking A-89frequency A-145gate A-14power A-145tuning A-242, A-257

tube amplifiers A-257tune command A-87, A-121, A-124, A-125, A-127,

A-193, A-196tune file A-87, A-121, A-125, A-126, A-193, A-196tuning knob A-146, A-147tuning the probehead A-51, A-134, A-135, A-136, A-

145, A-192, A-193, A-196

U

user definedAU programs A-70, A-81, A-172, A-264CPD programs A-15, A-176experiments A-194gradient files A-24gradient programs A-179, A-260

hard pulses A-87parameter sets A-163, A-164, A-165, A-260pulse programs A-40, A-177, A-188, A-215, A-

260, A-265relations file A-87shape files A-42soft pulses A-87XWIN-NMR settings A-282

User Interface A-173, A-176, A-179, A-188

V

variableamplitude list A-47, A-183, A-187counter list A-48, A-187, A-280dataset list A-19, A-187delay list A-49, A-180, A-187, A-280frequency list A-187, A-280pulse list A-49, A-187, A-280temperature list A-50, A-187, A-280

vish command A-130

W

well-plate A-56wide bore probe A-247, A-249, A-252wobb command A-51, A-134, A-136, A-145, A-192,

A-193, A-196, A-220wobble

curve A-51, A-146, A-192parameters A-135, A-137, A-148procedure A-146pulse program A-135, A-137, A-148steps A-51, A-148sweep width A-51, A-148

wpar command A-164, A-167wsh command A-130, A-131

X

xau command A-97, A-217, A-260xaua command A-13, A-194, A-197, A-217xaup command A-217XCMD macro A-5xfb command A-197Xwin-nmr

command sequence A-5display A-193, A-196, A-210, A-222

Index - xi

DONE

INDEX

INDEX

file handling A-3graphics A-284home directory A-4, A-63installation A-39, A-63, A-96, A-97, A-172, A-

188macros A-5, A-265menu A-6parameters A-7patchlevel A-286popup menus A-6resource settings A-282status line A-126version A-87, A-135, A-137, A-160, A-200, A-

202, A-210

Z

zg command A-7, A-8, A-11, A-192, A-200, A-220,A-221

Index - xii

DONE

INDEX

INDEX

Documents

Acquisition - Department of Chemistrycic/nmr/Guides/Bruker_AVANCE...This manual is written for Avance spectrometers. Nevertheless, a large part of it is also valid for older spectrometers